- GCR_STDERR - Static variable in class net.sourceforge.seqware.pipeline.modules.GenericCommandRunner
-
- GCR_STDERR_BUFFERSIZE - Static variable in class net.sourceforge.seqware.pipeline.modules.GenericCommandRunner
-
- GCR_STDOUT - Static variable in class net.sourceforge.seqware.pipeline.modules.GenericCommandRunner
-
- GCR_STDOUT_BUFFERSIZE - Static variable in class net.sourceforge.seqware.pipeline.modules.GenericCommandRunner
-
- generateDax(AbstractWorkflowDataModel, String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.DaxgeneratorV2
-
generate a dax file from the object model
- generateDaxFile(WorkflowInfo, File, String, Map<String, String>, List<String>) - Method in class net.sourceforge.seqware.pipeline.workflow.BasicWorkflow
-
generateDaxFile.
- generatedValue(String) - Static method in class net.sourceforge.seqware.common.util.maptools.MapTools
-
- generateLaneInfo(String, int) - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.BatchMetadataParser
-
Generates lane info with the given parameters.
- generateRunInfo(String, String, String, String, String, String, String, String, String, int, int, boolean, String, String) - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.BatchMetadataParser
-
Generates a RunInfo object with the given parameters.
- generateRunnerLine() - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object.OozieBashJob
-
- generateRunnerLine() - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object.OozieProvisionFileJob
-
- generateSampleInfo(String, String, String, String, String, String, String, String, String, int, String, String, String, String, String) - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.BatchMetadataParser
-
Generates a sample info object given the fields, and prompts for null
fields if the interactive flag is on.
- generateWorkflowXml(AbstractWorkflowDataModel, String, String, Path, boolean, File, String, String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.OozieWorkflowXmlGenerator
-
generate a dax file from the object model
- GenericCommandRunner - Class in net.sourceforge.seqware.pipeline.modules
-
This is a very simple module that takes a few options on the command line and
then passes the rest of the arguments to whatever command is specified.
- GenericCommandRunner() - Constructor for class net.sourceforge.seqware.pipeline.modules.GenericCommandRunner
-
- GenericDBResource - Class in net.sourceforge.seqware.webservice.resources.queries
-
GenericDBResource class.
- GenericDBResource(Context) - Constructor for class net.sourceforge.seqware.webservice.resources.queries.GenericDBResource
-
Constructor for GenericDBResource.
- GenericMetadataSaver - Class in net.sourceforge.seqware.pipeline.modules
-
Deprecated.
Deprecating this in favour of Metadata(plugin) and the new CLI
- GenericMetadataSaver() - Constructor for class net.sourceforge.seqware.pipeline.modules.GenericMetadataSaver
-
Deprecated.
- GEO_REACTION_ID_ATTR_TAG - Static variable in class net.sourceforge.seqware.common.model.Sample
-
The presence of this attribute is used to identify that the sample is a library
- get(Integer, Integer) - Method in interface net.sourceforge.seqware.common.business.FileAttributeService
-
get.
- get(Integer, Integer) - Method in class net.sourceforge.seqware.common.business.impl.FileAttributeServiceImpl
-
get.
- get(File) - Method in interface net.sourceforge.seqware.common.dao.FileAttributeDAO
-
get.
- get(Integer) - Method in interface net.sourceforge.seqware.common.dao.FileAttributeDAO
-
get.
- get(File) - Method in class net.sourceforge.seqware.common.dao.hibernate.FileAttributeDAOHibernate
-
get.
- get(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.FileAttributeDAOHibernate
-
get.
- get(Workflow) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowAttributeDAOHibernate
-
get.
- get(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowAttributeDAOHibernate
-
get.
- get(WorkflowRun) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowRunAttributeDAOHibernate
-
get.
- get(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowRunAttributeDAOHibernate
-
get.
- get(Workflow) - Method in interface net.sourceforge.seqware.common.dao.WorkflowAttributeDAO
-
get.
- get(Integer) - Method in interface net.sourceforge.seqware.common.dao.WorkflowAttributeDAO
-
get.
- get(WorkflowRun) - Method in interface net.sourceforge.seqware.common.dao.WorkflowRunAttributeDAO
-
get.
- get(Integer) - Method in interface net.sourceforge.seqware.common.dao.WorkflowRunAttributeDAO
-
get.
- get() - Static method in class net.sourceforge.seqware.common.factory.DBAccess
-
- get(Map<String, String>) - Static method in class net.sourceforge.seqware.common.metadata.MetadataFactory
-
- get() - Method in class net.sourceforge.seqware.webservice.resources.filters.WorkflowRunIDsFilter
- get() - Method in class net.sourceforge.seqware.webservice.resources.filters.WorkflowRunsFilter
- get() - Method in class net.sourceforge.seqware.webservice.resources.SeqwareAccessionIDResource
- get() - Method in class net.sourceforge.seqware.webservice.resources.SeqwareAccessionResource
- get() - Method in class net.sourceforge.seqware.webservice.resources.tables.StudyResource
- get_description() - Method in class io.seqware.pipeline.plugins.sanity.SanityCheck
-
get_description.
- get_description() - Method in interface net.sourceforge.seqware.pipeline.decider.DeciderInterface
-
Generates a short description of the plugin, preferably one line.
- get_description() - Method in class net.sourceforge.seqware.pipeline.deciders.BasicDecider
-
Generates a short description of the plugin, preferably one line.
- get_description() - Method in class net.sourceforge.seqware.pipeline.plugin.Plugin
-
Generates a short description of the plugin, preferably one line.
- get_description() - Method in interface net.sourceforge.seqware.pipeline.plugin.PluginInterface
-
Generates a short description of the plugin, preferably one line.
- get_description() - Method in class net.sourceforge.seqware.pipeline.plugin.WorkflowPlugin
-
- get_description() - Method in class net.sourceforge.seqware.pipeline.plugins.AttributeAnnotator
-
Generates a short description of the plugin, preferably one line.
- get_description() - Method in class net.sourceforge.seqware.pipeline.plugins.BatchMetadataInjection
-
Generates a short description of the plugin, preferably one line.
- get_description() - Method in class net.sourceforge.seqware.pipeline.plugins.BundleManager
-
get_description.
- get_description() - Method in class net.sourceforge.seqware.pipeline.plugins.checkdb.CheckDB
-
get_description.
- get_description() - Method in class net.sourceforge.seqware.pipeline.plugins.CycleChecker
-
Generates a short description of the plugin, preferably one line.
- get_description() - Method in class net.sourceforge.seqware.pipeline.plugins.deletion.DeletionDB
-
get_description.
- get_description() - Method in class net.sourceforge.seqware.pipeline.plugins.FileLinker
-
- get_description() - Method in class net.sourceforge.seqware.pipeline.plugins.fileprovenance.FileProvenanceReporter
-
- get_description() - Method in class net.sourceforge.seqware.pipeline.plugins.HelloWorld
-
get_description.
- get_description() - Method in class net.sourceforge.seqware.pipeline.plugins.MarkdownPlugin
-
get_description.
- get_description() - Method in class net.sourceforge.seqware.pipeline.plugins.Metadata
-
Generates a short description of the plugin, preferably one line.
- get_description() - Method in class net.sourceforge.seqware.pipeline.plugins.ModuleRunner
-
get_description.
- get_description() - Method in class net.sourceforge.seqware.pipeline.plugins.OozieXML2Dot
-
- get_description() - Method in class net.sourceforge.seqware.pipeline.plugins.ProcessingDataStructure2Dot
-
- get_description() - Method in class net.sourceforge.seqware.pipeline.plugins.SequencerRunReporter
-
Generates a short description of the plugin, preferably one line.
- get_description() - Method in class net.sourceforge.seqware.pipeline.plugins.SymLinkFileReporter
-
Generates a short description of the plugin, preferably one line.
- get_description() - Method in class net.sourceforge.seqware.pipeline.plugins.WorkflowRunFilesInitialPopulationPlugin
-
get_description.
- get_description() - Method in class net.sourceforge.seqware.pipeline.plugins.WorkflowRunReporter
-
Generates a short description of the plugin, preferably one line.
- get_description() - Method in class net.sourceforge.seqware.pipeline.plugins.WorkflowStatusChecker
-
Generates a short description of the plugin, preferably one line.
- get_galaxy_xml() - Method in class net.sourceforge.seqware.pipeline.module.Module
-
Output Galaxy definition files so you can use this module with Galaxy.
- get_syntax() - Method in interface net.sourceforge.seqware.pipeline.decider.DeciderInterface
-
Generates a "help" message for the user of the plugin.
- get_syntax() - Method in class net.sourceforge.seqware.pipeline.module.Module
-
Generates a "help" message for the user of the module.
- get_syntax() - Method in interface net.sourceforge.seqware.pipeline.module.ModuleInterface
-
Generates a "help" message for the user of the module.
- get_syntax() - Method in class net.sourceforge.seqware.pipeline.modules.GenericCommandRunner
-
Generates a "help" message for the user of the module.
- get_syntax() - Method in class net.sourceforge.seqware.pipeline.modules.GenericMetadataSaver
-
Deprecated.
Generates a "help" message for the user of the module.
- get_syntax() - Method in class net.sourceforge.seqware.pipeline.modules.utilities.ProvisionDependenciesBundle
-
get_syntax.
- get_syntax() - Method in class net.sourceforge.seqware.pipeline.modules.utilities.ProvisionFiles
-
get_syntax.
- get_syntax() - Method in class net.sourceforge.seqware.pipeline.modules.utilities.S3DeleteFiles
-
get_syntax.
- get_syntax() - Method in class net.sourceforge.seqware.pipeline.modules.utilities.S3ListFiles
-
get_syntax.
- get_syntax() - Method in class net.sourceforge.seqware.pipeline.modules.utilities.S3UploadDirectory
-
- get_syntax() - Method in class net.sourceforge.seqware.pipeline.plugin.Plugin
-
Generates a "help" message for the user of the plugin.
- get_syntax() - Method in interface net.sourceforge.seqware.pipeline.plugin.PluginInterface
-
Generates a "help" message for the user of the plugin.
- get_syntax() - Method in class net.sourceforge.seqware.pipeline.plugins.HelloWorld
-
Generates a "help" message for the user of the plugin.
- get_syntax() - Method in class net.sourceforge.seqware.pipeline.plugins.MarkdownPlugin
-
Generates a "help" message for the user of the plugin.
- get_syntax() - Method in class net.sourceforge.seqware.pipeline.plugins.WorkflowRunFilesInitialPopulationPlugin
-
Generates a "help" message for the user of the plugin.
- get_workflow_info(int) - Method in interface net.sourceforge.seqware.common.metadata.Metadata
-
get_workflow_info.
- get_workflow_info(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
-
get_workflow_info.
- get_workflow_info(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection
-
get_workflow_info.
- get_workflow_info(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS
-
get_workflow_info.
- get_workflow_run_accession(int) - Method in interface net.sourceforge.seqware.common.metadata.Metadata
-
get_workflow_run_accession.
- get_workflow_run_accession(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
-
get_workflow_run_accession.
- get_workflow_run_accession(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection
-
get_workflow_run_accession.
- get_workflow_run_accession(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS
-
get_workflow_run_accession.
- get_workflow_run_id(int) - Method in interface net.sourceforge.seqware.common.metadata.Metadata
-
get_workflow_run_id.
- get_workflow_run_id(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
-
get_workflow_run_id.
- get_workflow_run_id(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection
-
get_workflow_run_id.
- get_workflow_run_id(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS
-
get_workflow_run_id.
- getAbstract1() - Method in class io.seqware.webservice.generated.model.Study
-
- getAbstractStr() - Method in class net.sourceforge.seqware.common.model.Study
-
Getter for the field abstractStr.
- getAccession() - Method in class io.seqware.webservice.controller.ModelAccessionIDTuple
-
- getAccession() - Method in class io.seqware.webservice.generated.controller.ModelAccessionIDTuple
-
- getAccession() - Method in class io.seqware.webservice.generated.model.Experiment
-
- getAccession() - Method in class io.seqware.webservice.generated.model.Organism
-
- getAccession() - Method in class io.seqware.webservice.generated.model.Study
-
- getAccession() - Method in class net.sourceforge.seqware.common.model.Experiment
-
Getter for the field accession.
- getAccession() - Method in class net.sourceforge.seqware.common.model.Organism
-
Getter for the field accession.
- getAccession() - Method in class net.sourceforge.seqware.common.model.Study
-
Getter for the field accession.
- getAccessionFile() - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object.BatchedOozieBashJob
-
- getAccessionFile() - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object.BatchedOozieProvisionFileJob
-
- getAccessionFile() - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object.OozieJob
-
- getAccessionFile() - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object.PegasusJob
-
- getActive() - Method in class io.seqware.webservice.generated.model.ShareExperiment
-
- getActive() - Method in class io.seqware.webservice.generated.model.ShareFile
-
- getActive() - Method in class io.seqware.webservice.generated.model.ShareLane
-
- getActive() - Method in class io.seqware.webservice.generated.model.ShareProcessing
-
- getActive() - Method in class io.seqware.webservice.generated.model.ShareSample
-
- getActive() - Method in class io.seqware.webservice.generated.model.ShareStudy
-
- getActive() - Method in class io.seqware.webservice.generated.model.ShareWorkflowRun
-
- getActive() - Method in class net.sourceforge.seqware.common.model.ShareExperiment
-
Getter for the field active.
- getActive() - Method in class net.sourceforge.seqware.common.model.ShareFile
-
Getter for the field active.
- getActive() - Method in class net.sourceforge.seqware.common.model.ShareLane
-
Getter for the field active.
- getActive() - Method in class net.sourceforge.seqware.common.model.ShareProcessing
-
Getter for the field active.
- getActive() - Method in class net.sourceforge.seqware.common.model.ShareSample
-
Getter for the field active.
- getActive() - Method in class net.sourceforge.seqware.common.model.ShareStudy
-
Getter for the field active.
- getActive() - Method in class net.sourceforge.seqware.common.model.ShareWorkflowRun
-
Getter for the field active.
- getAdapters() - Method in class io.seqware.webservice.generated.model.Sample
-
- getAdapters() - Method in class net.sourceforge.seqware.common.model.Sample
-
Getter for the field
adapters.
- getAdapterSpec() - Method in class io.seqware.webservice.generated.model.ExperimentSpotDesign
-
- getAdapterSpec() - Method in class net.sourceforge.seqware.common.model.ExperimentSpotDesign
-
Getter for the field adapterSpec.
- getAddedSurcharge() - Method in class io.seqware.webservice.generated.model.Expense
-
- getAddedSurcharge() - Method in class net.sourceforge.seqware.common.model.Expense
-
Getter for the field
addedSurcharge.
- getAdminModelClass() - Method in class io.seqware.webservice.controller.ModelAccessionIDTuple
-
- getAdminModelClass() - Method in class io.seqware.webservice.generated.controller.ModelAccessionIDTuple
-
- getAgent() - Method in class io.seqware.webservice.generated.model.Expense
-
- getAgent() - Method in class net.sourceforge.seqware.common.model.Expense
-
Getter for the field
agent.
- getAlgo() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.AbstractJob
-
get the job algorithm
- getAlgorithm() - Method in class io.seqware.webservice.generated.model.Processing
-
- getAlgorithm() - Method in class net.sourceforge.seqware.common.model.Processing
-
Getter for the field algorithm.
- getAlgorithm() - Method in class net.sourceforge.seqware.common.module.ReturnValue
-
Getter for the field algorithm.
- getAlgorithm() - Method in class net.sourceforge.seqware.pipeline.module.Module
-
Getter for the field algorithm.
- getAlgorithm() - Method in interface net.sourceforge.seqware.pipeline.module.ModuleInterface
-
getAlgorithm.
- getAlgorithm() - Method in class net.sourceforge.seqware.pipeline.module.TestModule
-
Getter for the field algorithm.
- getAlias() - Method in class io.seqware.webservice.generated.model.Experiment
-
- getAlias() - Method in class io.seqware.webservice.generated.model.Ius
-
- getAlias() - Method in class io.seqware.webservice.generated.model.Lane
-
- getAlias() - Method in class io.seqware.webservice.generated.model.Sample
-
- getAlias() - Method in class io.seqware.webservice.generated.model.Study
-
- getAlias() - Method in class net.sourceforge.seqware.common.model.Experiment
-
Getter for the field alias.
- getAlias() - Method in class net.sourceforge.seqware.common.model.IUS
-
Getter for the field alias.
- getAlias() - Method in class net.sourceforge.seqware.common.model.Sample
-
Getter for the field
alias.
- getAlias() - Method in class net.sourceforge.seqware.common.model.Study
-
Getter for the field alias.
- getAlign() - Method in class net.sourceforge.solexatools.webapp.metamodel.Flexigrid.ColumnModel
-
- getAll() - Method in interface net.sourceforge.seqware.common.dao.FileAttributeDAO
-
getAll.
- getAll() - Method in class net.sourceforge.seqware.common.dao.hibernate.FileAttributeDAOHibernate
-
getAll.
- getAll() - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowAttributeDAOHibernate
-
getAll.
- getAll() - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowRunAttributeDAOHibernate
-
getAll.
- getAll() - Method in interface net.sourceforge.seqware.common.dao.WorkflowAttributeDAO
-
getAll.
- getAll() - Method in interface net.sourceforge.seqware.common.dao.WorkflowRunAttributeDAO
-
getAll.
- getAllHtml(Lane, Registration, String, String) - Static method in class net.sourceforge.solexatools.util.SequencerRunHtmlUtil
-
getAllHtml.
- getAllHtml(IUS, Registration, String, boolean, boolean, String) - Static method in class net.sourceforge.solexatools.util.SequencerRunHtmlUtil
-
getAllHtml.
- getAllHtml(Processing, Registration, String, Integer, List<String>, boolean, boolean, String) - Static method in class net.sourceforge.solexatools.util.SequencerRunHtmlUtil
-
getAllHtml.
- getAllHtml(Processing, Registration, String, Integer, List<String>, boolean, boolean, String) - Static method in class net.sourceforge.solexatools.util.StudyHtmlUtil
-
getAllHtml.
- getAllHtml(IUS, Registration, String, Integer, List<String>, boolean, boolean, String) - Static method in class net.sourceforge.solexatools.util.StudyHtmlUtil
-
getAllHtml.
- getAllHtml(Study, Registration, String) - Static method in class net.sourceforge.solexatools.util.TreeNodeHtmlUtil
-
getAllHtml.
- getAllHtml(Experiment, Registration, Integer, String) - Static method in class net.sourceforge.solexatools.util.TreeNodeHtmlUtil
-
getAllHtml.
- getAllHtml(Sample, Registration, Integer, String) - Static method in class net.sourceforge.solexatools.util.TreeNodeHtmlUtil
-
getAllHtml.
- getAllHtml(Lane, Registration, Integer, String) - Static method in class net.sourceforge.solexatools.util.TreeNodeHtmlUtil
-
getAllHtml.
- getAllInputFiles() - Method in class net.sourceforge.seqware.common.hibernate.reports.WorkflowRunReportRow
-
Getter for the field allInputFiles.
- getAllItems() - Method in class net.sourceforge.solexatools.util.PageInfo
-
Getter for the field allItems.
- getAllProcessing() - Method in class net.sourceforge.seqware.common.model.SequencerRun
-
getAllProcessing.
- getAllProcessings() - Method in class net.sourceforge.seqware.common.model.Lane
-
getAllProcessings.
- getAllRuns() - Method in class net.sourceforge.seqware.common.hibernate.WorkflowRunReport
-
Find all of the workflow runs, and report on each of the workflow runs
the files, samples and processing events associated with each.
- getAllSelectedFiles(HttpServletRequest) - Static method in class net.sourceforge.solexatools.util.LaunchWorkflowUtil
-
Get all selected Files, the files are organized by the name of the parameter (key) and a list of files selected (value) via a hash.
- getAllSequencerRuns() - Method in interface net.sourceforge.seqware.common.metadata.Metadata
-
Get all of the sequencer runs in the DB.
- getAllSequencerRuns() - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
-
- getAllSequencerRuns() - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection
-
- getAllSequencerRuns() - Method in class net.sourceforge.seqware.common.metadata.MetadataWS
-
getAllSequencerRuns.
- getAllStudies() - Method in interface net.sourceforge.seqware.common.metadata.Metadata
-
getAllStudies.
- getAllStudies() - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
-
getAllStudies.
- getAllStudies() - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection
-
getAllStudies.
- getAllStudies() - Method in class net.sourceforge.seqware.common.metadata.MetadataWS
-
getAllStudies.
- getAnalysisWorkflowHtml(WorkflowRun, Registration, String, boolean, boolean, String) - Static method in class net.sourceforge.solexatools.util.NodeHtmlUtil
-
getAnalysisWorkflowHtml.
- getAncestorWorkflowRunId() - Method in class io.seqware.webservice.generated.model.Processing
-
- getAnonymizedName() - Method in class io.seqware.webservice.generated.model.Sample
-
- getAnonymizedName() - Method in class net.sourceforge.seqware.common.model.Sample
-
Getter for the field
anonymizedName.
- getApplication() - Method in class net.sourceforge.seqware.webservice.resources.tables.WorkflowIDResource
- getApplicationInfo(Request, Response) - Method in class net.sourceforge.seqware.queryengine.webservice.controller.SeqWareWebServiceApplication
- getApplicationInfo(Request, Response) - Method in class net.sourceforge.seqware.queryengine.webservice.controller.SeqWareWebServiceApplicationVersion
- getArch() - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object.WorkflowExecutable
-
- getArguments() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Command
-
- getArguments() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.JobModule
-
Getter for the field arguments.
- getAssayType() - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.RunInfo
-
Get the value of assayType
- getAsText() - Method in class net.sourceforge.solexatools.validation.CustomIntegerEditor
-
getAsText.
- getAttribute(String) - Method in class net.sourceforge.seqware.common.module.ReturnValue
-
getAttribute.
- getAttribute() - Method in class net.sourceforge.seqware.webservice.resources.tables.DatabaseIDResource
-
Getter for the field attribute.
- getAttribute() - Method in interface net.sourceforge.seqware.webservice.resources.tables.FileAttributeResource
-
getAttribute.
- getAttribute() - Method in class net.sourceforge.seqware.webservice.resources.tables.FileAttributeServerResource
-
getAttribute.
- getAttributes() - Method in class net.sourceforge.seqware.common.module.ReturnValue
-
Getter for the field attributes.
- getAttributes() - Method in class net.sourceforge.seqware.webservice.dto.LibraryDto
-
Getter for the field attributes.
- getAttributes() - Method in class net.sourceforge.seqware.webservice.dto.SampleSearchDto
-
Getter for the field attributes.
- getBarcode() - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.SampleInfo
-
Get the value of barcode
- getBarcode() - Method in class net.sourceforge.seqware.webservice.dto.IusDto
-
Getter for the field barcode.
- getBaseCaller() - Method in class io.seqware.webservice.generated.model.Experiment
-
- getBaseCaller() - Method in class io.seqware.webservice.generated.model.SequencerRun
-
- getBaseCaller() - Method in class net.sourceforge.seqware.common.model.Experiment
-
Getter for the field baseCaller.
- getBaseCoord() - Method in class io.seqware.webservice.generated.model.ExperimentSpotDesignReadSpec
-
- getBaseCoord() - Method in class net.sourceforge.seqware.common.model.ExperimentSpotDesignReadSpec
-
Getter for the field baseCoord.
- getBaseDir() - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowInfo
-
Getter for the field baseDir.
- getBaseIniFile() - Method in class io.seqware.webservice.generated.model.Workflow
-
- getBaseIniFile() - Method in class net.sourceforge.seqware.common.model.Workflow
-
Getter for the field baseIniFile.
- getBatchedJobsCount() - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object.WorkflowApp.BucketGenerator
-
- getBatchSize() - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object.BatchedOozieBashJob
-
- getBatchSize() - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object.BatchedOozieProvisionFileJob
-
- getBundle_version() - Method in class net.sourceforge.seqware.pipeline.workflowV2.AbstractWorkflowDataModel
-
- getBundleInfo(File, File) - Method in class net.sourceforge.seqware.pipeline.bundle.Bundle
-
getBundleInfo.
- getCell() - Method in class net.sourceforge.solexatools.webapp.metamodel.Flexigrid.Cells
-
- getCenterName() - Method in class io.seqware.webservice.generated.model.Experiment
-
- getCenterName() - Method in class io.seqware.webservice.generated.model.Study
-
- getCenterName() - Method in class net.sourceforge.seqware.common.model.Experiment
-
Getter for the field centerName.
- getCenterName() - Method in class net.sourceforge.seqware.common.model.Study
-
Getter for the field centerName.
- getCenterProjectName() - Method in class io.seqware.webservice.generated.model.Study
-
- getCenterProjectName() - Method in class net.sourceforge.seqware.common.model.Study
-
Getter for the field centerProjectName.
- getChildId() - Method in class io.seqware.webservice.generated.model.ProcessingRelationship
-
- getChildId() - Method in class io.seqware.webservice.generated.model.SampleRelationship
-
- getChildren() - Method in class net.sourceforge.seqware.common.model.Processing
-
Getter for the field children.
- getChildren() - Method in class net.sourceforge.seqware.common.model.Sample
-
Getter for the field
children.
- getChildren() - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object.OozieJob
-
- getChildren() - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object.PegasusJob
-
- getChildrenUrls() - Method in class net.sourceforge.seqware.webservice.dto.LibraryDto
-
Getter for the field childrenUrls.
- getChildSample() - Method in class net.sourceforge.seqware.common.model.FileReportRow
-
Getter for the field childSample.
- getChildSample() - Method in class net.sourceforge.seqware.common.model.SampleReportRow
-
Getter for the field childSample.
- getChildSample() - Method in class net.sourceforge.seqware.common.model.SequencerRunReportId
-
Getter for the field childSample.
- getChildSample() - Method in class net.sourceforge.solexatools.webapp.metamodel.StudySampleReportFileLineItem
-
Getter for the field childSample.
- getChildSample() - Method in class net.sourceforge.solexatools.webapp.metamodel.StudySampleReportLineItem
-
Getter for the field childSample.
- getChildSampleId() - Method in class io.seqware.webservice.generated.model.FileReport
-
- getChildSampleId() - Method in class io.seqware.webservice.generated.model.SampleReport
-
- getChildSamples(Study) - Method in class net.sourceforge.seqware.common.business.impl.SampleReportServiceImpl
-
getChildSamples.
- getChildSamples(Study) - Method in interface net.sourceforge.seqware.common.business.SampleReportService
-
getChildSamples.
- getChildSamples(Study) - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleReportDAOHibernate
-
getChildSamples.
- getChildSamples(Study) - Method in interface net.sourceforge.seqware.common.dao.SampleReportDAO
-
getChildSamples.
- getChildSamplesFrom(int) - Method in interface net.sourceforge.seqware.common.metadata.Metadata
-
Get the child samples of a parent sample.
- getChildSamplesFrom(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
-
- getChildSamplesFrom(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection
-
- getChildSamplesFrom(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS
-
- getClassesDir() - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowInfo
-
Getter for the field classesDir.
- getClassPath() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.AbstractJob
-
- getClient() - Method in class io.seqware.webservice.generated.client.SeqWareWebserviceClient
-
- getClientNotes() - Method in class io.seqware.webservice.generated.model.Invoice
-
- getClientNotes() - Method in class net.sourceforge.seqware.common.model.Invoice
-
Getter for the field clientNotes.
- getCmd() - Method in class io.seqware.webservice.generated.model.Workflow
-
- getCmd() - Method in class io.seqware.webservice.generated.model.WorkflowRun
-
- getCode() - Method in class io.seqware.webservice.generated.model.LaneType
-
- getCode() - Method in class io.seqware.webservice.generated.model.Organism
-
- getCode() - Method in class net.sourceforge.seqware.common.model.Organism
-
Getter for the field code.
- getCode() - Method in class net.sourceforge.seqware.webservice.dto.OrganismDto
-
Getter for the field code.
- getColorMatrix() - Method in class io.seqware.webservice.generated.model.SequencerRun
-
- getColorMatrix() - Method in class net.sourceforge.seqware.common.model.SequencerRun
-
Getter for the field colorMatrix.
- getColorMatrix() - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
-
Getter for the field colorMatrix.
- getColorMatrixCode() - Method in class io.seqware.webservice.generated.model.SequencerRun
-
- getColorMatrixCode() - Method in class net.sourceforge.seqware.common.model.SequencerRun
-
Getter for the field colorMatrixCode.
- getColorMatrixCode() - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
-
Getter for the field colorMatrixCode.
- getCommand() - Method in class net.sourceforge.seqware.common.model.Workflow
-
Getter for the field command.
- getCommand() - Method in class net.sourceforge.seqware.common.model.WorkflowRun
-
Getter for the field command.
- getCommand() - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowInfo
-
Getter for the field command.
- getCommand() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.AbstractJob
-
- getCommand() - Method in interface net.sourceforge.seqware.pipeline.workflowV2.model.Job
-
- getCommand() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.JobBatch
-
- getCommonName() - Method in class io.seqware.webservice.generated.model.Sample
-
- getCompleted() - Method in class net.sourceforge.solexatools.webapp.metamodel.StudySampleReportLineItem
-
Getter for the field completed.
- getCompute() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Environment
-
- getComputeReq() - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowInfo
-
Getter for the field computeReq.
- getConfigPath() - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowInfo
-
Getter for the field configPath.
- getConfigs() - Method in class net.sourceforge.seqware.pipeline.workflowV2.AbstractWorkflowDataModel
-
- getConfiguration() - Method in class net.sourceforge.seqware.queryengine.webservice.controller.SeqWareWebServiceApplication
-
Getter for the field configuration.
- getConfiguration() - Method in class net.sourceforge.seqware.queryengine.webservice.controller.SeqWareWebServiceApplicationVersion
-
Getter for the field configuration.
- getConfirmEmailAddress() - Method in class net.sourceforge.seqware.common.model.RegistrationDTO
-
Getter for the field confirmEmailAddress.
- getConfirmPassword() - Method in class net.sourceforge.seqware.common.model.RegistrationDTO
-
Getter for the field confirmPassword.
- getConstructionProtocol() - Method in class io.seqware.webservice.generated.model.ExperimentLibraryDesign
-
- getConstructionProtocol() - Method in class net.sourceforge.seqware.common.model.ExperimentLibraryDesign
-
Getter for the field constructionProtocol.
- getCountFile() - Method in class net.sourceforge.seqware.common.model.Sample
-
Getter for the field
countFile.
- getCountFiles(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleDAOHibernate
-
getCountFiles.
- getCountFiles(Integer, String) - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleDAOHibernate
-
getCountFiles.
- getCountFiles(Integer) - Method in interface net.sourceforge.seqware.common.dao.SampleDAO
-
getCountFiles.
- getCountFiles(Integer, String) - Method in interface net.sourceforge.seqware.common.dao.SampleDAO
-
getCountFiles.
- getCreated() - Method in class net.sourceforge.seqware.common.model.SampleSearch
-
Getter for the field created.
- getCreateTimestamp() - Method in class net.sourceforge.seqware.common.model.Experiment
-
Getter for the field createTimestamp.
- getCreateTimestamp() - Method in class net.sourceforge.seqware.common.model.Invoice
-
Getter for the field createTimestamp.
- getCreateTimestamp() - Method in class net.sourceforge.seqware.common.model.IUS
-
Getter for the field createTimestamp.
- getCreateTimestamp() - Method in class net.sourceforge.seqware.common.model.Lane
-
Getter for the field createTimestamp.
- getCreateTimestamp() - Method in class net.sourceforge.seqware.common.model.Processing
-
Getter for the field createTimestamp.
- getCreateTimestamp() - Method in class net.sourceforge.seqware.common.model.Registration
-
Getter for the field createTimestamp.
- getCreateTimestamp() - Method in class net.sourceforge.seqware.common.model.Sample
-
Getter for the field
createTimestamp.
- getCreateTimestamp() - Method in class net.sourceforge.seqware.common.model.SequencerRun
-
Getter for the field createTimestamp.
- getCreateTimestamp() - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
-
Getter for the field createTimestamp.
- getCreateTimestamp() - Method in class net.sourceforge.seqware.common.model.ShareStudy
-
Getter for the field createTimestamp.
- getCreateTimestamp() - Method in class net.sourceforge.seqware.common.model.ShareWorkflowRun
-
Getter for the field createTimestamp.
- getCreateTimestamp() - Method in class net.sourceforge.seqware.common.model.Study
-
Getter for the field createTimestamp.
- getCreateTimestamp() - Method in class net.sourceforge.seqware.common.model.Workflow
-
Getter for the field createTimestamp.
- getCreateTimestamp() - Method in class net.sourceforge.seqware.common.model.WorkflowRun
-
Getter for the field createTimestamp.
- getCreateTimeStamp() - Method in class net.sourceforge.seqware.webservice.dto.IusDto
-
Getter for the field createTimeStamp.
- getCreateTimeStamp() - Method in class net.sourceforge.seqware.webservice.dto.LibraryDto
-
Getter for the field createTimeStamp.
- getCreateTstmp() - Method in class io.seqware.webservice.generated.model.Experiment
-
- getCreateTstmp() - Method in class io.seqware.webservice.generated.model.Invoice
-
- getCreateTstmp() - Method in class io.seqware.webservice.generated.model.Ius
-
- getCreateTstmp() - Method in class io.seqware.webservice.generated.model.Lane
-
- getCreateTstmp() - Method in class io.seqware.webservice.generated.model.Processing
-
- getCreateTstmp() - Method in class io.seqware.webservice.generated.model.Registration
-
- getCreateTstmp() - Method in class io.seqware.webservice.generated.model.Sample
-
- getCreateTstmp() - Method in class io.seqware.webservice.generated.model.SampleSearch
-
- getCreateTstmp() - Method in class io.seqware.webservice.generated.model.SequencerRun
-
- getCreateTstmp() - Method in class io.seqware.webservice.generated.model.ShareExperiment
-
- getCreateTstmp() - Method in class io.seqware.webservice.generated.model.ShareFile
-
- getCreateTstmp() - Method in class io.seqware.webservice.generated.model.ShareLane
-
- getCreateTstmp() - Method in class io.seqware.webservice.generated.model.ShareProcessing
-
- getCreateTstmp() - Method in class io.seqware.webservice.generated.model.ShareSample
-
- getCreateTstmp() - Method in class io.seqware.webservice.generated.model.ShareStudy
-
- getCreateTstmp() - Method in class io.seqware.webservice.generated.model.ShareWorkflowRun
-
- getCreateTstmp() - Method in class io.seqware.webservice.generated.model.Study
-
- getCreateTstmp() - Method in class io.seqware.webservice.generated.model.Workflow
-
- getCreateTstmp() - Method in class io.seqware.webservice.generated.model.WorkflowRun
-
- getCreateTstmp() - Method in class net.sourceforge.seqware.common.model.ShareExperiment
-
Getter for the field createTstmp.
- getCreateTstmp() - Method in class net.sourceforge.seqware.common.model.ShareFile
-
Getter for the field createTstmp.
- getCreateTstmp() - Method in class net.sourceforge.seqware.common.model.ShareLane
-
Getter for the field createTstmp.
- getCreateTstmp() - Method in class net.sourceforge.seqware.common.model.ShareProcessing
-
Getter for the field createTstmp.
- getCreateTstmp() - Method in class net.sourceforge.seqware.common.model.ShareSample
-
Getter for the field createTstmp.
- getCriteria() - Method in class net.sourceforge.solexatools.webapp.controller.SearchController
-
Getter for the field criteria.
- getCurrentBucket() - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object.WorkflowApp.BucketGenerator
-
- getCurrentSelectedFiles(HttpServletRequest) - Static method in class net.sourceforge.solexatools.util.LaunchWorkflowUtil
-
getCurrentSelectedFiles.
- getCurrentSelectedNodes(HttpServletRequest) - Static method in class net.sourceforge.solexatools.util.LaunchWorkflowUtil
-
getCurrentSelectedNodes.
- getCurrentWorkflow(HttpServletRequest) - Static method in class net.sourceforge.solexatools.util.LaunchWorkflowUtil
-
getCurrentWorkflow.
- getCurrentWorkflowParam(HttpServletRequest) - Static method in class net.sourceforge.solexatools.util.LaunchWorkflowUtil
-
getCurrentWorkflowParam.
- getCurrentWorkingDir() - Method in class io.seqware.webservice.generated.model.Workflow
-
- getCurrentWorkingDir() - Method in class io.seqware.webservice.generated.model.WorkflowRun
-
- getCurrentWorkingDir() - Method in class net.sourceforge.seqware.common.model.WorkflowRun
-
Getter for the field currentWorkingDir.
- getCwd() - Method in class net.sourceforge.seqware.common.model.Workflow
-
Getter for the field cwd.
- getCycleCoord() - Method in class io.seqware.webservice.generated.model.ExperimentSpotDesignReadSpec
-
- getCycleCoord() - Method in class net.sourceforge.seqware.common.model.ExperimentSpotDesignReadSpec
-
Getter for the field cycleCoord.
- getCycleCount() - Method in class io.seqware.webservice.generated.model.Lane
-
- getCycleCount() - Method in class io.seqware.webservice.generated.model.SequencerRun
-
- getCycleCount() - Method in class net.sourceforge.seqware.common.model.SequencerRun
-
Getter for the field cycleCount.
- getCycleCount() - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
-
Getter for the field cycleCount.
- getCycleDescriptor() - Method in class io.seqware.webservice.generated.model.Lane
-
- getCycleDescriptor() - Method in class io.seqware.webservice.generated.model.SequencerRun
-
- getCycleDescriptor() - Method in class net.sourceforge.seqware.common.model.Lane
-
Getter for the field cycleDescriptor.
- getCycleDescriptor() - Method in class net.sourceforge.seqware.common.model.SequencerRun
-
Getter for the field cycleDescriptor.
- getCycleDescriptor() - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
-
Getter for the field cycleDescriptor.
- getCycles() - Method in class net.sourceforge.seqware.common.model.SequencerRun
-
Getter for the field cycles.
- getCycles() - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
-
Getter for the field cycles.
- getCycleSequence() - Method in class io.seqware.webservice.generated.model.Lane
-
- getCycleSequence() - Method in class io.seqware.webservice.generated.model.SequencerRun
-
- getCycleSequence() - Method in class net.sourceforge.seqware.common.model.SequencerRun
-
Getter for the field cycleSequence.
- getCycleSequence() - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
-
Getter for the field cycleSequence.
- getDate() - Method in class net.sourceforge.seqware.common.hibernate.SequencerRunReport.Row
-
- getDate() - Method in class net.sourceforge.seqware.pipeline.workflowV2.AbstractWorkflowDataModel
-
- getDax() - Method in class io.seqware.webservice.generated.model.WorkflowRun
-
- getDax() - Method in class net.sourceforge.seqware.common.model.WorkflowRun
-
Getter for the field dax.
- getDaxDir() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Environment
-
- getDaysUntilDue() - Method in class io.seqware.webservice.generated.model.Invoice
-
- getDaysUntilDue() - Method in class net.sourceforge.seqware.common.model.Invoice
-
Getter for the field daysUntilDue.
- getDb() - Method in class io.seqware.webservice.generated.model.ExperimentLink
-
- getDb() - Method in class io.seqware.webservice.generated.model.IusLink
-
- getDb() - Method in class io.seqware.webservice.generated.model.LaneLink
-
- getDb() - Method in class io.seqware.webservice.generated.model.SampleLink
-
- getDb() - Method in class io.seqware.webservice.generated.model.StudyLink
-
- getDb() - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
-
Getter for the field
db.
- getDB(Map<String, String>) - Static method in class net.sourceforge.seqware.common.metadata.MetadataFactory
-
- getDb() - Method in class net.sourceforge.seqware.common.model.ExperimentLink
-
Getter for the field db.
- getDb() - Method in class net.sourceforge.seqware.common.model.IUSLink
-
Getter for the field db.
- getDb() - Method in class net.sourceforge.seqware.common.model.LaneLink
-
Getter for the field db.
- getDb() - Method in class net.sourceforge.seqware.common.model.SampleLink
-
Getter for the field db.
- getDb() - Method in class net.sourceforge.seqware.common.model.StudyLink
-
Getter for the field db.
- getDbmd() - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
-
Getter for the field
dbmd.
- getDecodeMethod() - Method in class io.seqware.webservice.generated.model.ExperimentSpotDesign
-
- getDecodeMethod() - Method in class net.sourceforge.seqware.common.model.ExperimentSpotDesign
-
Getter for the field decodeMethod.
- getDecryptCipher(String) - Method in class net.sourceforge.seqware.common.util.filetools.ProvisionFilesUtil
-
Gets cipher by DecryptKey.
- getDecryptCipher() - Method in class net.sourceforge.seqware.pipeline.modules.utilities.ProvisionFiles
-
getDecryptCipher.
- getDEFAULT_DB_HOST() - Method in class net.sourceforge.seqware.common.util.testtools.BasicTestDatabaseCreator
-
- getDEFAULT_DB_HOST() - Method in class net.sourceforge.seqware.metadb.util.TestDatabaseCreator
-
- getDEFAULT_DB_HOST() - Method in class net.sourceforge.seqware.pipeline.plugins.ExtendedTestDatabaseCreator
-
- getDefaultDirManagerExcutable(AbstractWorkflowDataModel) - Static method in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.WorkflowExecutableUtils
-
- getDefaultJavaExcutable(AbstractWorkflowDataModel) - Static method in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.WorkflowExecutableUtils
-
- getDefaultJavaLocalExcutable(AbstractWorkflowDataModel) - Static method in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.WorkflowExecutableUtils
-
- getDefaultPerlExcutable(AbstractWorkflowDataModel) - Static method in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.WorkflowExecutableUtils
-
- getDefaultValue() - Method in class io.seqware.webservice.generated.model.WorkflowParam
-
- getDefaultValue() - Method in class net.sourceforge.seqware.common.model.WorkflowParam
-
Getter for the field defaultValue.
- getDependentElement(PegasusJob) - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object.PegasusJob
-
- getDescription() - Method in class io.seqware.pipeline.plugins.sanity.checks.BundleDir_Check
-
- getDescription() - Method in class io.seqware.pipeline.plugins.sanity.checks.CLICheck
-
- getDescription() - Method in class io.seqware.pipeline.plugins.sanity.checks.DB_Check
-
- getDescription() - Method in class io.seqware.pipeline.plugins.sanity.checks.DB_WS_ConsistencyCheck
-
- getDescription() - Method in class io.seqware.pipeline.plugins.sanity.checks.HDFS_Check
-
- getDescription() - Method in class io.seqware.pipeline.plugins.sanity.checks.Oozie_Check
-
- getDescription() - Method in class io.seqware.pipeline.plugins.sanity.checks.Script_Check
-
- getDescription() - Method in class io.seqware.pipeline.plugins.sanity.checks.TutorialCheck
-
- getDescription() - Method in class io.seqware.pipeline.plugins.sanity.checks.WS_Check
-
- getDescription() - Method in interface io.seqware.pipeline.plugins.sanity.SanityCheckPluginInterface
-
Describes the check and indicates what may be wrong
- getDescription() - Method in class io.seqware.webservice.generated.model.Expense
-
- getDescription() - Method in class io.seqware.webservice.generated.model.Experiment
-
- getDescription() - Method in class io.seqware.webservice.generated.model.ExperimentLibraryDesign
-
- getDescription() - Method in class io.seqware.webservice.generated.model.File
-
- getDescription() - Method in class io.seqware.webservice.generated.model.Ius
-
- getDescription() - Method in class io.seqware.webservice.generated.model.Lane
-
- getDescription() - Method in class io.seqware.webservice.generated.model.LibrarySelection
-
- getDescription() - Method in class io.seqware.webservice.generated.model.LibrarySource
-
- getDescription() - Method in class io.seqware.webservice.generated.model.LibraryStrategy
-
- getDescription() - Method in class io.seqware.webservice.generated.model.Platform
-
- getDescription() - Method in class io.seqware.webservice.generated.model.Processing
-
- getDescription() - Method in class io.seqware.webservice.generated.model.ProcessingExperiments
-
- getDescription() - Method in class io.seqware.webservice.generated.model.ProcessingIus
-
- getDescription() - Method in class io.seqware.webservice.generated.model.ProcessingLanes
-
- getDescription() - Method in class io.seqware.webservice.generated.model.ProcessingSamples
-
- getDescription() - Method in class io.seqware.webservice.generated.model.ProcessingSequencerRuns
-
- getDescription() - Method in class io.seqware.webservice.generated.model.ProcessingStudies
-
- getDescription() - Method in class io.seqware.webservice.generated.model.Sample
-
- getDescription() - Method in class io.seqware.webservice.generated.model.SequencerRun
-
- getDescription() - Method in class io.seqware.webservice.generated.model.Study
-
- getDescription() - Method in class io.seqware.webservice.generated.model.StudyType
-
- getDescription() - Method in class io.seqware.webservice.generated.model.Workflow
-
- getDescription() - Method in class net.sourceforge.seqware.common.model.Expense
-
Getter for the field
description.
- getDescription() - Method in class net.sourceforge.seqware.common.model.Experiment
-
Getter for the field description.
- getDescription() - Method in class net.sourceforge.seqware.common.model.ExperimentLibraryDesign
-
Getter for the field description.
- getDescription() - Method in class net.sourceforge.seqware.common.model.File
-
Getter for the field description.
- getDescription() - Method in class net.sourceforge.seqware.common.model.IUS
-
Getter for the field description.
- getDescription() - Method in class net.sourceforge.seqware.common.model.Lane
-
Getter for the field description.
- getDescription() - Method in class net.sourceforge.seqware.common.model.LibrarySelection
-
Getter for the field description.
- getDescription() - Method in class net.sourceforge.seqware.common.model.LibrarySource
-
Getter for the field description.
- getDescription() - Method in class net.sourceforge.seqware.common.model.LibraryStrategy
-
Getter for the field description.
- getDescription() - Method in class net.sourceforge.seqware.common.model.Platform
-
Getter for the field description.
- getDescription() - Method in class net.sourceforge.seqware.common.model.Processing
-
Getter for the field description.
- getDescription() - Method in class net.sourceforge.seqware.common.model.ProcessingExperiments
-
Getter for the field description.
- getDescription() - Method in class net.sourceforge.seqware.common.model.ProcessingIus
-
Getter for the field description.
- getDescription() - Method in class net.sourceforge.seqware.common.model.ProcessingLanes
-
Getter for the field description.
- getDescription() - Method in class net.sourceforge.seqware.common.model.ProcessingSamples
-
Getter for the field description.
- getDescription() - Method in class net.sourceforge.seqware.common.model.ProcessingSequencerRuns
-
Getter for the field description.
- getDescription() - Method in class net.sourceforge.seqware.common.model.ProcessingStudies
-
Getter for the field description.
- getDescription() - Method in class net.sourceforge.seqware.common.model.Sample
-
Getter for the field
description.
- getDescription() - Method in class net.sourceforge.seqware.common.model.SequencerRun
-
Getter for the field description.
- getDescription() - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
-
Getter for the field description.
- getDescription() - Method in class net.sourceforge.seqware.common.model.Study
-
Getter for the field description.
- getDescription() - Method in class net.sourceforge.seqware.common.model.StudyType
-
Getter for the field description.
- getDescription() - Method in class net.sourceforge.seqware.common.model.Workflow
-
Getter for the field description.
- getDescription() - Method in class net.sourceforge.seqware.common.module.FileMetadata
-
- getDescription() - Method in class net.sourceforge.seqware.common.module.ReturnValue
-
Getter for the field description.
- getDescription() - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowInfo
-
Getter for the field description.
- getDescription() - Method in class net.sourceforge.seqware.webservice.dto.FileDto
-
Getter for the field description.
- getDescription() - Method in class net.sourceforge.seqware.webservice.dto.LibraryDto
-
Getter for the field description.
- getDeveloperMl() - Method in class io.seqware.webservice.generated.model.Registration
-
- getDirContext() - Method in class net.sourceforge.solexatools.authentication.OICRLdapAuthentication
-
getDirContext.
- getDirectories() - Method in class net.sourceforge.seqware.pipeline.workflowV2.AbstractWorkflowDataModel
-
- getDirectoriesNumber() - Method in class net.sourceforge.solexatools.util.FileFinder
-
Getter for the field directoriesNumber.
- getDirectorySize() - Method in class net.sourceforge.solexatools.util.FileFinder
-
getDirectorySize.
- getDisplay() - Method in class io.seqware.webservice.generated.model.WorkflowParam
-
- getDisplay() - Method in class net.sourceforge.seqware.common.model.WorkflowParam
-
Getter for the field display.
- getDisplay() - Method in class net.sourceforge.solexatools.webapp.metamodel.Flexigrid.ColumnModel
-
- getDisplayName() - Method in class io.seqware.webservice.generated.model.FileType
-
- getDisplayName() - Method in class io.seqware.webservice.generated.model.WorkflowParam
-
- getDisplayName() - Method in class io.seqware.webservice.generated.model.WorkflowParamValue
-
- getDisplayName() - Method in class net.sourceforge.seqware.common.model.FileType
-
Getter for the field displayName.
- getDisplayName() - Method in class net.sourceforge.seqware.common.model.WorkflowParam
-
Getter for the field displayName.
- getDisplayName() - Method in class net.sourceforge.seqware.common.model.WorkflowParamValue
-
Getter for the field displayName.
- getDisplayName() - Method in class net.sourceforge.solexatools.util.SummaryLine
-
Getter for the field displayName.
- getDisplayValue() - Method in class net.sourceforge.seqware.common.model.WorkflowParam
-
Getter for the field displayValue.
- getDomainObject() - Method in class net.sourceforge.seqware.common.model.RegistrationDTO
-
Getter for the field domainObject.
- getDomainObject() - Method in class net.sourceforge.seqware.common.model.SequencerRunWizardDTO
-
Getter for the field domainObject.
- getEmail() - Method in class io.seqware.webservice.generated.model.Registration
-
- getEmail() - Method in class net.sourceforge.seqware.webservice.dto.OwnerDto
-
Getter for the field email.
- getEmailAddress() - Method in class net.sourceforge.seqware.common.model.Registration
-
Getter for the field emailAddress.
- getEncryptCipher(String) - Method in class net.sourceforge.seqware.common.util.filetools.ProvisionFilesUtil
-
Gets cipher by EncryptKey.
- getEncryptCipher() - Method in class net.sourceforge.seqware.pipeline.modules.utilities.ProvisionFiles
-
getEncryptCipher.
- getEnd() - Method in class net.sourceforge.seqware.common.model.UploadSequence
-
Getter for the field end.
- getEndDate() - Method in class io.seqware.webservice.generated.model.Invoice
-
- getEndDate() - Method in class net.sourceforge.seqware.common.model.Invoice
-
Getter for the field endDate.
- getEndPage() - Method in class net.sourceforge.solexatools.util.PageInfo
-
Getter for the field endPage.
- getEntityManager() - Method in class io.seqware.webservice.generated.controller.AbstractFacade
-
- getEntityManager() - Method in class io.seqware.webservice.generated.controller.ExpenseAttributeFacadeREST
-
- getEntityManager() - Method in class io.seqware.webservice.generated.controller.ExpenseFacadeREST
-
- getEntityManager() - Method in class io.seqware.webservice.generated.controller.ExperimentAttributeFacadeREST
-
- getEntityManager() - Method in class io.seqware.webservice.generated.controller.ExperimentFacadeREST
-
- getEntityManager() - Method in class io.seqware.webservice.generated.controller.ExperimentLibraryDesignFacadeREST
-
- getEntityManager() - Method in class io.seqware.webservice.generated.controller.ExperimentLinkFacadeREST
-
- getEntityManager() - Method in class io.seqware.webservice.generated.controller.ExperimentSpotDesignFacadeREST
-
- getEntityManager() - Method in class io.seqware.webservice.generated.controller.ExperimentSpotDesignReadSpecFacadeREST
-
- getEntityManager() - Method in class io.seqware.webservice.generated.controller.FileAttributeFacadeREST
-
- getEntityManager() - Method in class io.seqware.webservice.generated.controller.FileFacadeREST
-
- getEntityManager() - Method in class io.seqware.webservice.generated.controller.FileReportFacadeREST
-
- getEntityManager() - Method in class io.seqware.webservice.generated.controller.FileTypeFacadeREST
-
- getEntityManager() - Method in class io.seqware.webservice.generated.controller.InvoiceAttributeFacadeREST
-
- getEntityManager() - Method in class io.seqware.webservice.generated.controller.InvoiceFacadeREST
-
- getEntityManager() - Method in class io.seqware.webservice.generated.controller.IusAttributeFacadeREST
-
- getEntityManager() - Method in class io.seqware.webservice.generated.controller.IusFacadeREST
-
- getEntityManager() - Method in class io.seqware.webservice.generated.controller.IusLinkFacadeREST
-
- getEntityManager() - Method in class io.seqware.webservice.generated.controller.IusWorkflowRunsFacadeREST
-
- getEntityManager() - Method in class io.seqware.webservice.generated.controller.LaneAttributeFacadeREST
-
- getEntityManager() - Method in class io.seqware.webservice.generated.controller.LaneFacadeREST
-
- getEntityManager() - Method in class io.seqware.webservice.generated.controller.LaneLinkFacadeREST
-
- getEntityManager() - Method in class io.seqware.webservice.generated.controller.LaneTypeFacadeREST
-
- getEntityManager() - Method in class io.seqware.webservice.generated.controller.LaneWorkflowRunsFacadeREST
-
- getEntityManager() - Method in class io.seqware.webservice.generated.controller.LibrarySelectionFacadeREST
-
- getEntityManager() - Method in class io.seqware.webservice.generated.controller.LibrarySourceFacadeREST
-
- getEntityManager() - Method in class io.seqware.webservice.generated.controller.LibraryStrategyFacadeREST
-
- getEntityManager() - Method in class io.seqware.webservice.generated.controller.OrganismFacadeREST
-
- getEntityManager() - Method in class io.seqware.webservice.generated.controller.PlatformFacadeREST
-
- getEntityManager() - Method in class io.seqware.webservice.generated.controller.ProcessingAttributeFacadeREST
-
- getEntityManager() - Method in class io.seqware.webservice.generated.controller.ProcessingExperimentsFacadeREST
-
- getEntityManager() - Method in class io.seqware.webservice.generated.controller.ProcessingFacadeREST
-
- getEntityManager() - Method in class io.seqware.webservice.generated.controller.ProcessingFilesFacadeREST
-
- getEntityManager() - Method in class io.seqware.webservice.generated.controller.ProcessingIusFacadeREST
-
- getEntityManager() - Method in class io.seqware.webservice.generated.controller.ProcessingLanesFacadeREST
-
- getEntityManager() - Method in class io.seqware.webservice.generated.controller.ProcessingRelationshipFacadeREST
-
- getEntityManager() - Method in class io.seqware.webservice.generated.controller.ProcessingSamplesFacadeREST
-
- getEntityManager() - Method in class io.seqware.webservice.generated.controller.ProcessingSequencerRunsFacadeREST
-
- getEntityManager() - Method in class io.seqware.webservice.generated.controller.ProcessingStudiesFacadeREST
-
- getEntityManager() - Method in class io.seqware.webservice.generated.controller.RegistrationFacadeREST
-
- getEntityManager() - Method in class io.seqware.webservice.generated.controller.SampleAttributeFacadeREST
-
- getEntityManager() - Method in class io.seqware.webservice.generated.controller.SampleFacadeREST
-
- getEntityManager() - Method in class io.seqware.webservice.generated.controller.SampleLinkFacadeREST
-
- getEntityManager() - Method in class io.seqware.webservice.generated.controller.SampleRelationshipFacadeREST
-
- getEntityManager() - Method in class io.seqware.webservice.generated.controller.SampleReportFacadeREST
-
- getEntityManager() - Method in class io.seqware.webservice.generated.controller.SampleSearchAttributeFacadeREST
-
- getEntityManager() - Method in class io.seqware.webservice.generated.controller.SampleSearchFacadeREST
-
- getEntityManager() - Method in class io.seqware.webservice.generated.controller.SequencerRunAttributeFacadeREST
-
- getEntityManager() - Method in class io.seqware.webservice.generated.controller.SequencerRunFacadeREST
-
- getEntityManager() - Method in class io.seqware.webservice.generated.controller.ShareExperimentFacadeREST
-
- getEntityManager() - Method in class io.seqware.webservice.generated.controller.ShareFileFacadeREST
-
- getEntityManager() - Method in class io.seqware.webservice.generated.controller.ShareLaneFacadeREST
-
- getEntityManager() - Method in class io.seqware.webservice.generated.controller.ShareProcessingFacadeREST
-
- getEntityManager() - Method in class io.seqware.webservice.generated.controller.ShareSampleFacadeREST
-
- getEntityManager() - Method in class io.seqware.webservice.generated.controller.ShareStudyFacadeREST
-
- getEntityManager() - Method in class io.seqware.webservice.generated.controller.ShareWorkflowRunFacadeREST
-
- getEntityManager() - Method in class io.seqware.webservice.generated.controller.StudyAttributeFacadeREST
-
- getEntityManager() - Method in class io.seqware.webservice.generated.controller.StudyFacadeREST
-
- getEntityManager() - Method in class io.seqware.webservice.generated.controller.StudyLinkFacadeREST
-
- getEntityManager() - Method in class io.seqware.webservice.generated.controller.StudyTypeFacadeREST
-
- getEntityManager() - Method in class io.seqware.webservice.generated.controller.WorkflowAttributeFacadeREST
-
- getEntityManager() - Method in class io.seqware.webservice.generated.controller.WorkflowFacadeREST
-
- getEntityManager() - Method in class io.seqware.webservice.generated.controller.WorkflowParamFacadeREST
-
- getEntityManager() - Method in class io.seqware.webservice.generated.controller.WorkflowParamValueFacadeREST
-
- getEntityManager() - Method in class io.seqware.webservice.generated.controller.WorkflowRunAttributeFacadeREST
-
- getEntityManager() - Method in class io.seqware.webservice.generated.controller.WorkflowRunFacadeREST
-
- getEntityManager() - Method in class io.seqware.webservice.generated.controller.WorkflowRunParamFacadeREST
-
- getEntityUrl() - Method in class net.sourceforge.seqware.webservice.dto.AttributeDto
-
Getter for the field entityUrl.
- getEnv() - Method in class net.sourceforge.seqware.pipeline.workflowV2.AbstractWorkflowDataModel
-
- getError() - Method in class net.sourceforge.seqware.common.util.iotools.BufferedReaderThread
-
Getter for the field error.
- getErrorCnt(SequencerRun) - Method in class net.sourceforge.seqware.common.dao.hibernate.SequencerRunDAOHibernate
-
getErrorCnt.
- getErrorCnt(SequencerRun) - Method in interface net.sourceforge.seqware.common.dao.SequencerRunDAO
-
Deprecated.
- getErrorCnt() - Method in class net.sourceforge.seqware.common.model.Lane
-
getErrorCnt.
- getErrorCnt() - Method in class net.sourceforge.seqware.common.model.SequencerRun
-
getErrorCnt.
- getErrorCnt() - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
-
getErrorCnt.
- getErrorCount() - Method in class net.sourceforge.seqware.common.model.SequencerRun
-
Getter for the field errorCount.
- getExecutionEnv() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Environment
-
- getExistingType() - Method in class io.seqware.webservice.generated.model.Study
-
- getExistingType() - Method in class net.sourceforge.seqware.common.model.Study
-
Getter for the field existingType.
- getExistingTypeInt() - Method in class net.sourceforge.seqware.common.model.Study
-
Getter for the field existingTypeInt.
- getExitCode() - Method in exception net.sourceforge.seqware.common.err.OldSeqwareException
-
getExitCode.
- getExitCode() - Method in exception net.sourceforge.seqware.common.err.SeqwareException
-
getExitCode.
- getExitCode() - Method in exception net.sourceforge.seqware.common.err.SwBadFileException
-
getExitCode.
- getExitCode() - Method in exception net.sourceforge.seqware.common.err.SwBadModuleException
-
getExitCode.
- getExitCode() - Method in exception net.sourceforge.seqware.common.err.SwParameterException
-
getExitCode.
- getExitCode() - Method in exception net.sourceforge.seqware.common.err.SwRunnerParameterException
-
getExitCode.
- getExitStatus() - Method in class io.seqware.webservice.generated.model.Processing
-
- getExitStatus() - Method in class net.sourceforge.seqware.common.model.Processing
-
Getter for the field exitStatus.
- getExitStatus() - Method in class net.sourceforge.seqware.common.module.ReturnValue
-
Getter for the field exitStatus.
- getExpectedBasecall() - Method in class io.seqware.webservice.generated.model.ExperimentSpotDesignReadSpec
-
- getExpectedBaseCall() - Method in class net.sourceforge.seqware.common.model.ExperimentSpotDesignReadSpec
-
Getter for the field expectedBaseCall.
- getExpectedNumberReads() - Method in class io.seqware.webservice.generated.model.Experiment
-
- getExpectedNumberReads() - Method in class io.seqware.webservice.generated.model.Sample
-
- getExpectedNumberReads() - Method in class net.sourceforge.seqware.common.model.Experiment
-
Getter for the field expectedNumberReads.
- getExpectedNumberRuns() - Method in class io.seqware.webservice.generated.model.Experiment
-
- getExpectedNumberRuns() - Method in class io.seqware.webservice.generated.model.Sample
-
- getExpectedNumberRuns() - Method in class net.sourceforge.seqware.common.model.Experiment
-
Getter for the field expectedNumberRuns.
- getExpectedNumberSpots() - Method in class io.seqware.webservice.generated.model.Experiment
-
- getExpectedNumberSpots() - Method in class io.seqware.webservice.generated.model.Sample
-
- getExpectedNumberSpots() - Method in class net.sourceforge.seqware.common.model.Experiment
-
Getter for the field expectedNumberSpots.
- getExpectedNumReads() - Method in class net.sourceforge.seqware.common.model.Sample
-
Getter for the field
expectedNumReads.
- getExpectedNumRuns() - Method in class net.sourceforge.seqware.common.model.Sample
-
Getter for the field
expectedNumRuns.
- getExpectedNumSpots() - Method in class net.sourceforge.seqware.common.model.Sample
-
Getter for the field
expectedNumSpots.
- getExpenseAttributeCollection() - Method in class io.seqware.webservice.generated.model.Expense
-
- getExpenseAttributeId() - Method in class io.seqware.webservice.generated.model.ExpenseAttribute
-
- getExpenseCollection() - Method in class io.seqware.webservice.generated.model.Invoice
-
- getExpenseFinishedTstmp() - Method in class io.seqware.webservice.generated.model.Expense
-
- getExpenseId() - Method in class io.seqware.webservice.generated.model.Expense
-
- getExpenseId() - Method in class io.seqware.webservice.generated.model.ExpenseAttribute
-
- getExpenseId() - Method in class net.sourceforge.seqware.common.model.Expense
-
Getter for the field
expenseId.
- getExpenses() - Method in class net.sourceforge.seqware.common.model.Invoice
-
Getter for the field expenses.
- getExpenseType() - Method in class io.seqware.webservice.generated.model.Expense
-
- getExpenseType() - Method in class net.sourceforge.seqware.common.model.Expense
-
Getter for the field
expenseType.
- getExperiment(int) - Method in interface net.sourceforge.seqware.common.metadata.Metadata
-
getExperiment.
- getExperiment(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
-
- getExperiment(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection
-
- getExperiment(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS
-
- getExperiment() - Method in class net.sourceforge.seqware.common.model.ExperimentAttribute
-
Getter for the field experiment.
- getExperiment() - Method in class net.sourceforge.seqware.common.model.ExperimentLink
-
Getter for the field experiment.
- getExperiment() - Method in class net.sourceforge.seqware.common.model.FileReportRow
-
Getter for the field experiment.
- getExperiment() - Method in class net.sourceforge.seqware.common.model.ProcessingExperiments
-
Getter for the field experiment.
- getExperiment() - Method in class net.sourceforge.seqware.common.model.Sample
-
Getter for the field
experiment.
- getExperiment() - Method in class net.sourceforge.seqware.common.model.ShareExperiment
-
Getter for the field experiment.
- getExperimentAttributeCollection() - Method in class io.seqware.webservice.generated.model.Experiment
-
- getExperimentAttributeId() - Method in class io.seqware.webservice.generated.model.ExperimentAttribute
-
- getExperimentAttributeId() - Method in class net.sourceforge.seqware.common.model.ExperimentAttribute
-
Getter for the field experimentAttributeId.
- getExperimentAttributes() - Method in class net.sourceforge.seqware.common.model.Experiment
-
Getter for the field experimentAttributes.
- getExperimentAttributes() - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.RunInfo
-
Get the value of experimentAttributes
- getExperimentCollection() - Method in class io.seqware.webservice.generated.model.ExperimentLibraryDesign
-
- getExperimentCollection() - Method in class io.seqware.webservice.generated.model.ExperimentSpotDesign
-
- getExperimentCollection() - Method in class io.seqware.webservice.generated.model.Platform
-
- getExperimentCollection() - Method in class io.seqware.webservice.generated.model.Registration
-
- getExperimentCollection() - Method in class io.seqware.webservice.generated.model.Study
-
- getExperimentDescription() - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.RunInfo
-
Get the value of experimentDescription
- getExperimentHtml(Experiment, Registration, String, String, boolean, String) - Static method in class net.sourceforge.solexatools.util.NodeHtmlUtil
-
getExperimentHtml.
- getExperimentId() - Method in class io.seqware.webservice.generated.model.Experiment
-
- getExperimentId() - Method in class io.seqware.webservice.generated.model.ExperimentAttribute
-
- getExperimentId() - Method in class io.seqware.webservice.generated.model.ExperimentLink
-
- getExperimentId() - Method in class io.seqware.webservice.generated.model.FileReport
-
- getExperimentId() - Method in class io.seqware.webservice.generated.model.ProcessingExperiments
-
- getExperimentId() - Method in class io.seqware.webservice.generated.model.Sample
-
- getExperimentId() - Method in class io.seqware.webservice.generated.model.ShareExperiment
-
- getExperimentId() - Method in class net.sourceforge.seqware.common.model.Experiment
-
Getter for the field experimentId.
- getExperimentLibraryDesign() - Method in class net.sourceforge.seqware.common.model.Experiment
-
Getter for the field experimentLibraryDesign.
- getExperimentLibraryDesignCollection() - Method in class io.seqware.webservice.generated.model.LibrarySelection
-
- getExperimentLibraryDesignCollection() - Method in class io.seqware.webservice.generated.model.LibrarySource
-
- getExperimentLibraryDesignCollection() - Method in class io.seqware.webservice.generated.model.LibraryStrategy
-
- getExperimentLibraryDesignId() - Method in class io.seqware.webservice.generated.model.Experiment
-
- getExperimentLibraryDesignId() - Method in class io.seqware.webservice.generated.model.ExperimentLibraryDesign
-
- getExperimentLibraryDesignId() - Method in class net.sourceforge.seqware.common.model.ExperimentLibraryDesign
-
Getter for the field experimentLibraryDesignId.
- getExperimentLibraryDesigns() - Method in interface net.sourceforge.seqware.common.metadata.Metadata
-
getExperimentLibraryDesigns.
- getExperimentLibraryDesigns() - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
-
- getExperimentLibraryDesigns() - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection
-
- getExperimentLibraryDesigns() - Method in class net.sourceforge.seqware.common.metadata.MetadataWS
-
- getExperimentLibraryDesignService() - Method in class net.sourceforge.seqware.common.ContextImpl
-
- getExperimentLibraryDesignService() - Method in class net.sourceforge.solexatools.webapp.controller.ExperimentController
-
Getter for the field experimentLibraryDesignService.
- getExperimentLibraryDesignServiceBean() - Static method in class net.sourceforge.seqware.common.factory.BeanFactory
-
- getExperimentLinkCollection() - Method in class io.seqware.webservice.generated.model.Experiment
-
- getExperimentLinkId() - Method in class io.seqware.webservice.generated.model.ExperimentLink
-
- getExperimentLinkId() - Method in class net.sourceforge.seqware.common.model.ExperimentLink
-
Getter for the field experimentLinkId.
- getExperimentLinks() - Method in class net.sourceforge.seqware.common.model.Experiment
-
Getter for the field experimentLinks.
- getExperimentName() - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.RunInfo
-
Get the value of experimentName
- getExperiments() - Method in class net.sourceforge.seqware.common.model.Processing
-
Getter for the field experiments.
- getExperiments() - Method in class net.sourceforge.seqware.common.model.Study
-
Getter for the field experiments.
- getExperimentService() - Method in class net.sourceforge.seqware.common.ContextImpl
-
Getter for the field experimentService.
- getExperimentService() - Method in class net.sourceforge.solexatools.validation.ExperimentValidator
-
Getter for the field experimentService.
- getExperimentService() - Method in class net.sourceforge.solexatools.webapp.controller.BulkDownloadListDetailsController
-
Getter for the field experimentService.
- getExperimentService() - Method in class net.sourceforge.solexatools.webapp.controller.DownloadFileListController
-
Getter for the field experimentService.
- getExperimentService() - Method in class net.sourceforge.solexatools.webapp.controller.ExperimentController
-
Getter for the field experimentService.
- getExperimentService() - Method in class net.sourceforge.solexatools.webapp.controller.ExperimentSetupController
-
Getter for the field experimentService.
- getExperimentService() - Method in class net.sourceforge.solexatools.webapp.controller.LaunchWorkflowListDetailsController
-
Getter for the field experimentService.
- getExperimentService() - Method in class net.sourceforge.solexatools.webapp.controller.SampleController
-
Getter for the field experimentService.
- getExperimentService() - Method in class net.sourceforge.solexatools.webapp.controller.SampleSetupController
-
Getter for the field experimentService.
- getExperimentService() - Method in class net.sourceforge.solexatools.webapp.controller.SaveOpenNodeController
-
Getter for the field experimentService.
- getExperimentService() - Method in class net.sourceforge.solexatools.webapp.controller.SelectInputListController
-
Getter for the field experimentService.
- getExperimentService() - Method in class net.sourceforge.solexatools.webapp.controller.StudyListDetailsController
-
Getter for the field experimentService.
- getExperimentService() - Method in class net.sourceforge.solexatools.webapp.controller.StudyListDetailsFlatController
-
Getter for the field experimentService.
- getExperimentService() - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileController
-
Getter for the field experimentService.
- getExperimentService() - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileSetupController
-
Getter for the field experimentService.
- getExperimentServiceBean() - Static method in class net.sourceforge.seqware.common.factory.BeanFactory
-
getExperimentServiceBean.
- getExperimentsFrom(int) - Method in interface net.sourceforge.seqware.common.metadata.Metadata
-
Get experiments from a study.
- getExperimentsFrom(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
-
- getExperimentsFrom(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection
-
- getExperimentsFrom(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS
-
- getExperimentSpotDesign() - Method in class net.sourceforge.seqware.common.model.Experiment
-
Getter for the field experimentSpotDesign.
- getExperimentSpotDesign() - Method in class net.sourceforge.seqware.common.model.ExperimentSpotDesignReadSpec
-
Getter for the field experimentSpotDesign.
- getExperimentSpotDesignId() - Method in class io.seqware.webservice.generated.model.Experiment
-
- getExperimentSpotDesignId() - Method in class io.seqware.webservice.generated.model.ExperimentSpotDesign
-
- getExperimentSpotDesignId() - Method in class io.seqware.webservice.generated.model.ExperimentSpotDesignReadSpec
-
- getExperimentSpotDesignId() - Method in class net.sourceforge.seqware.common.model.ExperimentSpotDesign
-
Getter for the field experimentSpotDesignId.
- getExperimentSpotDesignReadSpecCollection() - Method in class io.seqware.webservice.generated.model.ExperimentSpotDesign
-
- getExperimentSpotDesignReadSpecId() - Method in class io.seqware.webservice.generated.model.ExperimentSpotDesignReadSpec
-
- getExperimentSpotDesignReadSpecId() - Method in class net.sourceforge.seqware.common.model.ExperimentSpotDesignReadSpec
-
Getter for the field experimentSpotDesignReadSpecId.
- getExperimentSpotDesignReadSpecs() - Method in interface net.sourceforge.seqware.common.metadata.Metadata
-
getPlatforms.
- getExperimentSpotDesignReadSpecs() - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
-
- getExperimentSpotDesignReadSpecs() - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection
-
- getExperimentSpotDesignReadSpecs() - Method in class net.sourceforge.seqware.common.metadata.MetadataWS
-
- getExperimentSpotDesignReadSpecService() - Method in class net.sourceforge.seqware.common.ContextImpl
-
- getExperimentSpotDesignReadSpecService() - Method in class net.sourceforge.solexatools.webapp.controller.ExperimentController
-
Getter for the field experimentSpotDesignReadSpecService.
- getExperimentSpotDesignReadSpecServiceBean() - Static method in class net.sourceforge.seqware.common.factory.BeanFactory
-
- getExperimentSpotDesigns() - Method in interface net.sourceforge.seqware.common.metadata.Metadata
-
getExperimentSpotDesigns.
- getExperimentSpotDesigns() - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
-
- getExperimentSpotDesigns() - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection
-
- getExperimentSpotDesigns() - Method in class net.sourceforge.seqware.common.metadata.MetadataWS
-
- getExperimentSpotDesignService() - Method in class net.sourceforge.seqware.common.ContextImpl
-
- getExperimentSpotDesignService() - Method in class net.sourceforge.solexatools.webapp.controller.ExperimentController
-
Getter for the field experimentSpotDesignService.
- getExperimentSpotDesignServiceBean() - Static method in class net.sourceforge.seqware.common.factory.BeanFactory
-
- getExperimentSwas() - Method in class net.sourceforge.seqware.common.business.impl.ValidationReportServiceImpl.ReportEntry
-
- getExpLibDesignDesc() - Method in class net.sourceforge.seqware.common.model.Experiment
-
Getter for the field expLibDesignDesc.
- getExpLibDesignName() - Method in class net.sourceforge.seqware.common.model.Experiment
-
Getter for the field expLibDesignName.
- getExpLibDesignProtocol() - Method in class net.sourceforge.seqware.common.model.Experiment
-
Getter for the field expLibDesignProtocol.
- getExpLibDesignSelection() - Method in class net.sourceforge.seqware.common.model.Experiment
-
Getter for the field expLibDesignSelection.
- getExpLibDesignSource() - Method in class net.sourceforge.seqware.common.model.Experiment
-
Getter for the field expLibDesignSource.
- getExpLibDesignStrategy() - Method in class net.sourceforge.seqware.common.model.Experiment
-
Getter for the field expLibDesignStrategy.
- getExpSpotDesignAdapterSpec() - Method in class net.sourceforge.seqware.common.model.Experiment
-
Getter for the field expSpotDesignAdapterSpec.
- getExpSpotDesignReadsPerSpot() - Method in class net.sourceforge.seqware.common.model.Experiment
-
Getter for the field expSpotDesignReadsPerSpot.
- getExpSpotDesignTagSpec() - Method in class net.sourceforge.seqware.common.model.Experiment
-
Getter for the field expSpotDesignTagSpec.
- getExtension() - Method in class io.seqware.webservice.generated.model.FileType
-
- getExtension() - Method in class net.sourceforge.seqware.common.model.FileType
-
Getter for the field extension.
- getExtension(String) - Method in class net.sourceforge.solexatools.validation.UploadFileValidator
-
getExtension.
- getExternalId() - Method in class io.seqware.webservice.generated.model.Invoice
-
- getExternalId() - Method in class net.sourceforge.seqware.common.model.Invoice
-
Getter for the field externalId.
- getFailed() - Method in class net.sourceforge.solexatools.webapp.metamodel.StudySampleReportLineItem
-
Getter for the field failed.
- getFailedCount(Study) - Method in class net.sourceforge.seqware.common.business.impl.StudyServiceImpl
-
getFailedCount.
- getFailedCount(Study) - Method in interface net.sourceforge.seqware.common.business.StudyService
-
getFailedCount.
- getFailedJobsInfo(String) - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowTools
-
This method will examine a Pegasus DAX log directory for a given workflow
and identify the log files for jobs that failed.
- getFile() - Method in class net.sourceforge.seqware.common.business.UploadFile
-
Getter for the field file.
- getFile(int) - Method in interface net.sourceforge.seqware.common.metadata.Metadata
-
getFile.
- getFile(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
-
getFile.
- getFile(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection
-
getFile.
- getFile(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS
-
getFile.
- getFile() - Method in class net.sourceforge.seqware.common.model.FileAttribute
-
Getter for the field file.
- getFile() - Method in class net.sourceforge.seqware.common.model.FileReportRow
-
Getter for the field file.
- getFile() - Method in class net.sourceforge.seqware.common.model.ShareFile
-
Getter for the field file.
- getFile() - Method in class net.sourceforge.solexatools.webapp.metamodel.StudySampleReportFileLineItem
-
Getter for the field file.
- getFileAttributeCollection() - Method in class io.seqware.webservice.generated.model.File
-
- getFileAttributeId() - Method in class io.seqware.webservice.generated.model.FileAttribute
-
- getFileAttributeId() - Method in class net.sourceforge.seqware.common.model.FileAttribute
-
Getter for the field fileAttributeId.
- getFileAttributes(Integer) - Method in interface net.sourceforge.seqware.common.business.FileAttributeService
-
Returns a complete set of attributes for a give File.
- getFileAttributes(Integer) - Method in class net.sourceforge.seqware.common.business.impl.FileAttributeServiceImpl
-
Returns a complete set of attributes for a give File.
- getFileAttributes() - Method in class net.sourceforge.seqware.common.model.File
-
Getter for the field fileAttributes.
- getFileAttributes() - Method in interface net.sourceforge.seqware.webservice.resources.tables.FileAttributesResource
-
getFileAttributes.
- getFileAttributes() - Method in class net.sourceforge.seqware.webservice.resources.tables.FileAttributesServerResource
-
getFileAttributes.
- getFileAttributeService() - Method in class net.sourceforge.seqware.common.ContextImpl
-
Getter for the field fileAttributeService.
- getFileAttributeServiceBean() - Static method in class net.sourceforge.seqware.common.factory.BeanFactory
-
getFileAttributeServiceBean.
- getFileCollection() - Method in class io.seqware.webservice.generated.model.FileType
-
- getFileCollection() - Method in class io.seqware.webservice.generated.model.Registration
-
- getFileCollection() - Method in class io.seqware.webservice.generated.model.WorkflowRun
-
- getFileHtml(Processing, Registration) - Static method in class net.sourceforge.solexatools.util.SequencerRunHtmlUtil
-
getFileHtml.
- getFileHtml(Processing, Registration, List<String>, String) - Static method in class net.sourceforge.solexatools.util.StudyHtmlUtil
-
getFileHtml.
- getFileHtml(Processing, WorkflowRun, Registration, String) - Static method in class net.sourceforge.solexatools.util.WorkflowRunHtmlUtil
-
getFileHtml.
- getFileId() - Method in class io.seqware.webservice.generated.model.File
-
- getFileId() - Method in class io.seqware.webservice.generated.model.FileAttribute
-
- getFileId() - Method in class io.seqware.webservice.generated.model.FileReport
-
- getFileId() - Method in class io.seqware.webservice.generated.model.ProcessingFiles
-
- getFileId() - Method in class io.seqware.webservice.generated.model.ShareFile
-
- getFileId() - Method in class net.sourceforge.seqware.common.model.File
-
Getter for the field fileId.
- getFileMetaType() - Method in class io.seqware.webservice.generated.model.WorkflowParam
-
- getFileMetaType() - Method in class net.sourceforge.seqware.common.model.WorkflowParam
-
Getter for the field fileMetaType.
- getFileMetaType() - Method in class net.sourceforge.solexatools.util.SummaryLine
-
Getter for the field fileMetaType.
- getFilename() - Method in class net.sourceforge.seqware.common.business.impl.ValidationReportServiceImpl.ReportEntry
-
- getFileName() - Method in class net.sourceforge.seqware.common.model.File
-
getFileName.
- getFilename(String) - Static method in class net.sourceforge.seqware.common.util.filetools.FileTools
-
- getFileName() - Method in class net.sourceforge.seqware.common.util.filetools.ProvisionFilesUtil
-
Gets the file name.
- getFilename() - Method in class net.sourceforge.seqware.pipeline.plugins.filelinker.FileLinkerLine
-
- getFileName(String) - Method in class net.sourceforge.solexatools.webapp.controller.LoadIndexPageController
-
getFileName.
- getFileOne() - Method in class net.sourceforge.seqware.common.model.UploadSequence
-
Getter for the field fileOne.
- getFilePath() - Method in class io.seqware.webservice.generated.model.File
-
- getFilePath() - Method in class io.seqware.webservice.generated.model.SequencerRun
-
- getFilePath() - Method in class net.sourceforge.seqware.common.model.File
-
Getter for the field filePath.
- getFilePath() - Method in class net.sourceforge.seqware.common.model.Processing
-
Getter for the field filePath.
- getFilePath() - Method in class net.sourceforge.seqware.common.model.SequencerRun
-
Getter for the field filePath.
- getFilePath() - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
-
Getter for the field filePath.
- getFilePath() - Method in class net.sourceforge.seqware.common.module.FileMetadata
-
- getFilePath(String) - Static method in class net.sourceforge.seqware.common.util.filetools.FileTools
-
- getFilePath(int) - Method in class net.sourceforge.seqware.queryengine.webservice.model.MetadataDB
-
getFilePath.
- getFilePath() - Method in class net.sourceforge.seqware.webservice.dto.FileDto
-
Getter for the field filePath.
- getFiles(Integer) - Method in interface net.sourceforge.seqware.common.business.ExperimentService
-
getFiles.
- getFiles(Integer, String) - Method in interface net.sourceforge.seqware.common.business.ExperimentService
-
getFiles.
- getFiles(Integer) - Method in interface net.sourceforge.seqware.common.business.FileService
-
getFiles.
- getFiles(Integer, String) - Method in interface net.sourceforge.seqware.common.business.FileService
-
getFiles.
- getFiles(Integer) - Method in class net.sourceforge.seqware.common.business.impl.ExperimentServiceImpl
-
getFiles.
- getFiles(Integer, String) - Method in class net.sourceforge.seqware.common.business.impl.ExperimentServiceImpl
-
getFiles.
- getFiles(Integer) - Method in class net.sourceforge.seqware.common.business.impl.FileServiceImpl
-
getFiles.
- getFiles(Integer, String) - Method in class net.sourceforge.seqware.common.business.impl.FileServiceImpl
-
getFiles.
- getFiles(Integer) - Method in class net.sourceforge.seqware.common.business.impl.IUSServiceImpl
-
getFiles.
- getFiles(Integer, String) - Method in class net.sourceforge.seqware.common.business.impl.IUSServiceImpl
-
getFiles.
- getFiles(Integer) - Method in class net.sourceforge.seqware.common.business.impl.LaneServiceImpl
-
getFiles.
- getFiles(Integer, String) - Method in class net.sourceforge.seqware.common.business.impl.LaneServiceImpl
-
getFiles.
- getFiles(Integer) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingServiceImpl
-
getFiles.
- getFiles(Integer, String) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingServiceImpl
-
getFiles.
- getFiles(Integer) - Method in class net.sourceforge.seqware.common.business.impl.SampleServiceImpl
-
getFiles.
- getFiles(Integer, String) - Method in class net.sourceforge.seqware.common.business.impl.SampleServiceImpl
-
getFiles.
- getFiles(Integer) - Method in class net.sourceforge.seqware.common.business.impl.StudyServiceImpl
-
getFiles.
- getFiles(Integer, String) - Method in class net.sourceforge.seqware.common.business.impl.StudyServiceImpl
-
getFiles.
- getFiles(Integer) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowRunServiceImpl
-
getFiles.
- getFiles(Integer) - Method in interface net.sourceforge.seqware.common.business.IUSService
-
getFiles.
- getFiles(Integer, String) - Method in interface net.sourceforge.seqware.common.business.IUSService
-
getFiles.
- getFiles(Integer) - Method in interface net.sourceforge.seqware.common.business.LaneService
-
getFiles.
- getFiles(Integer, String) - Method in interface net.sourceforge.seqware.common.business.LaneService
-
getFiles.
- getFiles(Integer) - Method in interface net.sourceforge.seqware.common.business.ProcessingService
-
getFiles.
- getFiles(Integer, String) - Method in interface net.sourceforge.seqware.common.business.ProcessingService
-
getFiles.
- getFiles(Integer) - Method in interface net.sourceforge.seqware.common.business.SampleService
-
getFiles.
- getFiles(Integer, String) - Method in interface net.sourceforge.seqware.common.business.SampleService
-
getFiles.
- getFiles(Integer) - Method in interface net.sourceforge.seqware.common.business.StudyService
-
getFiles.
- getFiles(Integer, String) - Method in interface net.sourceforge.seqware.common.business.StudyService
-
getFiles.
- getFiles(Integer) - Method in interface net.sourceforge.seqware.common.business.WorkflowRunService
-
getFiles.
- getFiles(Integer) - Method in interface net.sourceforge.seqware.common.dao.ExperimentDAO
-
getFiles.
- getFiles(Integer, String) - Method in interface net.sourceforge.seqware.common.dao.ExperimentDAO
-
getFiles.
- getFiles(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.ExperimentDAOHibernate
-
getFiles.
- getFiles(Integer, String) - Method in class net.sourceforge.seqware.common.dao.hibernate.ExperimentDAOHibernate
-
getFiles.
- getFiles(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.IUSDAOHibernate
-
getFiles.
- getFiles(Integer, String) - Method in class net.sourceforge.seqware.common.dao.hibernate.IUSDAOHibernate
-
getFiles.
- getFiles(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.LaneDAOHibernate
-
getFiles.
- getFiles(Integer, String) - Method in class net.sourceforge.seqware.common.dao.hibernate.LaneDAOHibernate
-
getFiles.
- getFiles(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.ProcessingDAOHibernate
-
getFiles.
- getFiles(Integer, String) - Method in class net.sourceforge.seqware.common.dao.hibernate.ProcessingDAOHibernate
-
getFiles.
- getFiles(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleDAOHibernate
-
getFiles.
- getFiles(Integer, String) - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleDAOHibernate
-
getFiles.
- getFiles(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.StudyDAOHibernate
-
getFiles.
- getFiles(Integer, String) - Method in class net.sourceforge.seqware.common.dao.hibernate.StudyDAOHibernate
-
getFiles.
- getFiles(Integer) - Method in interface net.sourceforge.seqware.common.dao.IUSDAO
-
getFiles.
- getFiles(Integer, String) - Method in interface net.sourceforge.seqware.common.dao.IUSDAO
-
getFiles.
- getFiles(Integer) - Method in interface net.sourceforge.seqware.common.dao.LaneDAO
-
getFiles.
- getFiles(Integer, String) - Method in interface net.sourceforge.seqware.common.dao.LaneDAO
-
getFiles.
- getFiles(Integer) - Method in interface net.sourceforge.seqware.common.dao.ProcessingDAO
-
getFiles.
- getFiles(Integer, String) - Method in interface net.sourceforge.seqware.common.dao.ProcessingDAO
-
getFiles.
- getFiles(Integer) - Method in interface net.sourceforge.seqware.common.dao.SampleDAO
-
getFiles.
- getFiles(Integer, String) - Method in interface net.sourceforge.seqware.common.dao.SampleDAO
-
getFiles.
- getFiles(Integer) - Method in interface net.sourceforge.seqware.common.dao.StudyDAO
-
getFiles.
- getFiles(Integer, String) - Method in interface net.sourceforge.seqware.common.dao.StudyDAO
-
getFiles.
- getFiles() - Method in class net.sourceforge.seqware.common.model.Processing
-
Getter for the field files.
- getFiles() - Method in class net.sourceforge.seqware.common.model.WorkflowParam
-
Getter for the field files.
- getFiles() - Method in class net.sourceforge.seqware.common.module.ReturnValue
-
Getter for the field files.
- getFiles() - Method in class net.sourceforge.seqware.pipeline.workflowV2.AbstractWorkflowDataModel
-
- getFiles() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.AbstractJob
-
- getFiles(HttpServletRequest, String) - Static method in class net.sourceforge.solexatools.util.BulkUtil
-
getFiles.
- getFiles() - Method in class net.sourceforge.solexatools.util.SummaryLine
-
Getter for the field files.
- getFiles_url() - Method in class net.sourceforge.seqware.webservice.dto.IusDto
-
Getter for the field files_url.
- getFilesArray() - Method in class net.sourceforge.seqware.pipeline.bundle.Bundle
-
Getter for the field filesArray.
- getFileService() - Method in class net.sourceforge.seqware.common.ContextImpl
-
Getter for the field fileService.
- getFileService() - Method in class net.sourceforge.solexatools.validation.UploadFileValidator
-
Getter for the field fileService.
- getFileService() - Method in class net.sourceforge.solexatools.validation.UploadSequenceValidator
-
Getter for the field fileService.
- getFileService() - Method in class net.sourceforge.solexatools.webapp.controller.BulkDownloaderController
-
Getter for the field fileService.
- getFileService() - Method in class net.sourceforge.solexatools.webapp.controller.BulkDownloadListDetailsController
-
Getter for the field fileService.
- getFileService() - Method in class net.sourceforge.solexatools.webapp.controller.DownloaderController
-
Getter for the field fileService.
- getFileService() - Method in class net.sourceforge.solexatools.webapp.controller.DownloadFileListController
-
Getter for the field fileService.
- getFileService() - Method in class net.sourceforge.solexatools.webapp.controller.FileController
-
Getter for the field fileService.
- getFileService() - Method in class net.sourceforge.solexatools.webapp.controller.FileSetupController
-
Getter for the field fileService.
- getFileService() - Method in class net.sourceforge.solexatools.webapp.controller.LaunchWorkflowListDetailsController
-
Getter for the field fileService.
- getFileService() - Method in class net.sourceforge.solexatools.webapp.controller.LoadIndexPageController
-
Getter for the field fileService.
- getFileService() - Method in class net.sourceforge.solexatools.webapp.controller.SaveOpenNodeController
-
Getter for the field fileService.
- getFileService() - Method in class net.sourceforge.solexatools.webapp.controller.SelectInputListController
-
Getter for the field fileService.
- getFileService() - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileController
-
Getter for the field fileService.
- getFileService() - Method in class net.sourceforge.solexatools.webapp.controller.UploadSequenceController
-
Getter for the field fileService.
- getFileServiceBean() - Static method in class net.sourceforge.seqware.common.factory.BeanFactory
-
getFileServiceBean.
- getFileSize(String) - Static method in class net.sourceforge.seqware.common.util.filetools.ProvisionFilesUtil
-
getFileSize.
- getFilesNumber() - Method in class net.sourceforge.solexatools.util.FileFinder
-
Getter for the field filesNumber.
- getFileStatus() - Method in class net.sourceforge.seqware.pipeline.plugins.filelinker.FileLinkerLine
-
- getFileSwa() - Method in class net.sourceforge.seqware.common.business.impl.ValidationReportServiceImpl.ReportEntry
-
- getFileTwo() - Method in class net.sourceforge.seqware.common.model.UploadSequence
-
Getter for the field fileTwo.
- getFileTwoURL() - Method in class net.sourceforge.seqware.common.model.UploadSequence
-
Getter for the field fileTwoURL.
- getFileType() - Method in class net.sourceforge.seqware.common.business.UploadFile
-
Getter for the field fileType.
- getFileType() - Method in class net.sourceforge.seqware.common.model.File
-
Getter for the field fileType.
- getFileType() - Method in class net.sourceforge.seqware.common.model.UploadSequence
-
Getter for the field fileType.
- getFileTypeId() - Method in class io.seqware.webservice.generated.model.File
-
- getFileTypeId() - Method in class io.seqware.webservice.generated.model.FileType
-
- getFileTypeId() - Method in class net.sourceforge.seqware.common.business.UploadFile
-
Getter for the field fileTypeId.
- getFileTypeId() - Method in class net.sourceforge.seqware.common.model.FileType
-
Getter for the field fileTypeId.
- getFileTypeId() - Method in class net.sourceforge.seqware.common.model.UploadSequence
-
Getter for the field fileTypeId.
- getFileTypeService() - Method in class net.sourceforge.solexatools.validation.UploadFileValidator
-
Getter for the field fileTypeService.
- getFileTypeService() - Method in class net.sourceforge.solexatools.validation.UploadSequenceValidator
-
Getter for the field fileTypeService.
- getFileTypeService() - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileController
-
Getter for the field fileTypeService.
- getFileTypeService() - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileSetupController
-
Getter for the field fileTypeService.
- getFileTypeService() - Method in class net.sourceforge.solexatools.webapp.controller.UploadSequenceController
-
Getter for the field fileTypeService.
- getFileTypeService() - Method in class net.sourceforge.solexatools.webapp.controller.UploadSequenceSetupController
-
Getter for the field fileTypeService.
- getFileUploadService() - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileController
-
Getter for the field fileUploadService.
- getFileURL() - Method in class net.sourceforge.seqware.common.business.UploadFile
-
Getter for the field fileURL.
- getFileURL() - Method in class net.sourceforge.seqware.common.model.UploadSequence
-
Getter for the field fileURL.
- getFileValidationServiceBean() - Static method in class net.sourceforge.seqware.common.factory.BeanFactory
-
getFileValidationServiceBean.
- getFinalized() - Method in class io.seqware.webservice.generated.model.Invoice
-
- getFinishedCount(Study) - Method in class net.sourceforge.seqware.common.business.impl.StudyServiceImpl
-
getFinishedCount.
- getFinishedCount(Study) - Method in interface net.sourceforge.seqware.common.business.StudyService
-
getFinishedCount.
- getFinishedTimestamp() - Method in class net.sourceforge.seqware.common.model.Expense
-
Getter for the field
finishedTimestamp.
- getFirstId(String) - Static method in class net.sourceforge.solexatools.util.Constant
-
getFirstId.
- getFirstName() - Method in class io.seqware.webservice.generated.model.Registration
-
- getFirstName() - Method in class net.sourceforge.seqware.common.model.Registration
-
Getter for the field firstName.
- getFirstName() - Method in class net.sourceforge.seqware.webservice.dto.OwnerDto
-
Getter for the field firstName.
- getFlowCount() - Method in class io.seqware.webservice.generated.model.SequencerRun
-
- getFlowCount() - Method in class net.sourceforge.seqware.common.model.SequencerRun
-
Getter for the field flowCount.
- getFlowCount() - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
-
Getter for the field flowCount.
- getFlowSequence() - Method in class io.seqware.webservice.generated.model.SequencerRun
-
- getFlowSequence() - Method in class net.sourceforge.seqware.common.model.SequencerRun
-
Getter for the field flowSequence.
- getFlowSequence() - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
-
Getter for the field flowSequence.
- getFolderStore() - Method in class net.sourceforge.seqware.common.business.UploadFile
-
Getter for the field folderStore.
- getFolderStore() - Method in class net.sourceforge.seqware.common.model.UploadSequence
-
Getter for the field folderStore.
- getForceRunAll() - Method in class net.sourceforge.seqware.pipeline.deciders.BasicDecider
-
- getFs_default_name() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Environment
-
- getFs_defaultFS() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Environment
-
- getFs_hdfs_impl() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Environment
-
- getFullName() - Method in class net.sourceforge.seqware.common.model.Workflow
-
getFullName.
- getFullyPaid() - Method in class io.seqware.webservice.generated.model.Invoice
-
- getGcrOutputFile() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Command
-
- getGroupingStrategy() - Method in class net.sourceforge.seqware.pipeline.deciders.BasicDecider
-
- getHbase_master() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Environment
-
- getHbase_zookeeper_property_clientPort() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Environment
-
- getHbase_zookeeper_quorum() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Environment
-
- getHeader() - Method in class net.sourceforge.seqware.pipeline.deciders.BasicDecider
-
Deprecated.
- getHeader() - Method in class net.sourceforge.seqware.webservice.resources.queries.WorkflowRunReportResource
-
getHeader.
- getHost() - Method in class io.seqware.webservice.generated.model.Workflow
-
- getHost() - Method in class io.seqware.webservice.generated.model.WorkflowRun
-
- getHost() - Method in class net.sourceforge.seqware.common.model.Workflow
-
Deprecated.
- getHost() - Method in class net.sourceforge.seqware.common.model.WorkflowRun
-
Getter for the field host.
- getHost() - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowInfo
-
Getter for the field host.
- getHtml() - Method in class net.sourceforge.seqware.common.model.SequencerRun
-
Getter for the field html.
- getHtml() - Method in class net.sourceforge.seqware.common.model.Study
-
Getter for the field html.
- getHtml() - Method in class net.sourceforge.seqware.common.model.WorkflowRun
-
Getter for the field html.
- getHtml(Object, Registration, List<String>, String) - Static method in class net.sourceforge.solexatools.util.SequencerRunHtmlUtil
-
getHtml.
- getHtml(Object, Registration, List<String>, String) - Static method in class net.sourceforge.solexatools.util.StudyHtmlUtil
-
getHtml.
- getHtml(Object, Registration, String) - Static method in class net.sourceforge.solexatools.util.TreeNodeHtmlUtil
-
getHtml.
- getHtml(WorkflowRun, Registration, String, boolean, String) - Static method in class net.sourceforge.solexatools.util.WorkflowRunHtmlUtil
-
getHtml.
- getHtml(Sample, WorkflowRun, Registration, String) - Static method in class net.sourceforge.solexatools.util.WorkflowRunHtmlUtil
-
getHtml.
- getHtml(Processing, WorkflowRun, Registration, String, List<String>, String) - Static method in class net.sourceforge.solexatools.util.WorkflowRunHtmlUtil
-
getHtml.
- getHttpInputStream(String, int, long) - Method in class net.sourceforge.seqware.common.util.filetools.ProvisionFilesUtil
-
getHttpInputStream.
- getId() - Method in class io.seqware.webservice.controller.ModelAccessionIDTuple
-
- getId() - Method in class io.seqware.webservice.generated.controller.ModelAccessionIDTuple
-
- getId() - Method in class io.seqware.webservice.generated.model.ExperimentLink
-
- getId() - Method in class io.seqware.webservice.generated.model.IusLink
-
- getId() - Method in class io.seqware.webservice.generated.model.LaneLink
-
- getId() - Method in class io.seqware.webservice.generated.model.SampleLink
-
- getId() - Method in class io.seqware.webservice.generated.model.StudyLink
-
- getId() - Method in class net.sourceforge.seqware.common.business.UploadFile
-
Getter for the field id.
- getId() - Method in class net.sourceforge.seqware.common.model.ExperimentLink
-
Getter for the field id.
- getId() - Method in class net.sourceforge.seqware.common.model.IUSLink
-
Getter for the field id.
- getId() - Method in class net.sourceforge.seqware.common.model.LaneLink
-
Getter for the field id.
- getId() - Method in class net.sourceforge.seqware.common.model.SampleLink
-
Getter for the field id.
- getId() - Method in class net.sourceforge.seqware.common.model.StudyLink
-
Getter for the field id.
- getId() - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object.PegasusJob
-
get the job id
- getId() - Method in class net.sourceforge.seqware.webservice.resources.tables.DatabaseIDResource
-
Getter for the field id.
- getId(String) - Static method in class net.sourceforge.solexatools.util.Constant
-
getId.
- getIdentitySamples() - Method in class net.sourceforge.seqware.common.hibernate.reports.WorkflowRunReportRow
-
Getter for the field identitySamples.
- getIdsSelectedLane(HttpServletRequest, WorkflowParam) - Method in class net.sourceforge.solexatools.util.LaunchWorkflowUtil
-
getIdsSelectedLane.
- getImmediateInputFiles() - Method in class net.sourceforge.seqware.common.hibernate.reports.WorkflowRunReportRow
-
Getter for the field immediateInputFiles.
- getIndividualName() - Method in class io.seqware.webservice.generated.model.Sample
-
- getIndividualName() - Method in class net.sourceforge.seqware.common.model.Sample
-
Getter for the field
individualName.
- getIndividualNumber() - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.SampleInfo
-
- getInfo() - Method in class net.sourceforge.seqware.common.model.FileType
-
getInfo.
- getInfo() - Method in class net.sourceforge.solexatools.util.PageInfo
-
Getter for the field info.
- getIniFile() - Method in class io.seqware.webservice.generated.model.WorkflowRun
-
- getIniFile() - Method in class net.sourceforge.seqware.common.model.WorkflowRun
-
Getter for the field iniFile.
- getInputAlgorithm() - Method in class io.seqware.webservice.generated.model.Workflow
-
- getInputAlgorithm() - Method in class net.sourceforge.seqware.common.model.Workflow
-
Getter for the field inputAlgorithm.
- getInputFileAccessions() - Method in class net.sourceforge.seqware.common.model.WorkflowRun
-
- getInstance() - Static method in class net.sourceforge.seqware.common.ContextImpl
-
getInstance.
- getInstance() - Static method in class net.sourceforge.seqware.common.util.runtools.ConsoleAdapter
-
- getInstitution() - Method in class io.seqware.webservice.generated.model.Registration
-
- getInstitution() - Method in class net.sourceforge.seqware.common.model.Registration
-
Getter for the field institution.
- getInstitution() - Method in class net.sourceforge.seqware.webservice.dto.OwnerDto
-
Getter for the field institution.
- getInstrumentModel() - Method in class io.seqware.webservice.generated.model.Platform
-
- getInstrumentModel() - Method in class net.sourceforge.seqware.common.model.Platform
-
Getter for the field instrumentModel.
- getInstrumentName() - Method in class io.seqware.webservice.generated.model.SequencerRun
-
- getInstrumentName() - Method in class net.sourceforge.seqware.common.model.SequencerRun
-
Getter for the field instrumentName.
- getInstrumentName() - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
-
Getter for the field instrumentName.
- getInvitationCode() - Method in class io.seqware.webservice.generated.model.Registration
-
- getInvitationCode() - Method in class net.sourceforge.seqware.common.model.Registration
-
Getter for the field invitationCode.
- getInvoice() - Method in class net.sourceforge.seqware.common.model.Expense
-
Getter for the field
invoice.
- getInvoiceAttributeCollection() - Method in class io.seqware.webservice.generated.model.Invoice
-
- getInvoiceAttributeId() - Method in class io.seqware.webservice.generated.model.InvoiceAttribute
-
- getInvoiceCollection() - Method in class io.seqware.webservice.generated.model.Registration
-
- getInvoiceId() - Method in class io.seqware.webservice.generated.model.Expense
-
- getInvoiceId() - Method in class io.seqware.webservice.generated.model.Invoice
-
- getInvoiceId() - Method in class io.seqware.webservice.generated.model.InvoiceAttribute
-
- getInvoiceId() - Method in class net.sourceforge.seqware.common.model.Invoice
-
Getter for the field invoiceId.
- getInvoiceService() - Method in class net.sourceforge.solexatools.webapp.controller.InvoiceDetailsController
-
Getter for the field invoiceService.
- getInvoiceService() - Method in class net.sourceforge.solexatools.webapp.controller.OpenInvoiceController
-
Getter for the field invoiceService.
- getIsEnd() - Method in class net.sourceforge.solexatools.util.PageInfo
-
Getter for the field isEnd.
- getIsHasFile() - Method in class net.sourceforge.seqware.common.model.Experiment
-
Getter for the field isHasFile.
- getIsHasFile() - Method in class net.sourceforge.seqware.common.model.IUS
-
Getter for the field isHasFile.
- getIsHasFile() - Method in class net.sourceforge.seqware.common.model.Lane
-
Getter for the field isHasFile.
- getIsHasFile() - Method in class net.sourceforge.seqware.common.model.Processing
-
Getter for the field isHasFile.
- getIsHasFile() - Method in class net.sourceforge.seqware.common.model.Sample
-
Getter for the field
isHasFile.
- getIsHasFile() - Method in class net.sourceforge.seqware.common.model.Study
-
Getter for the field isHasFile.
- getIsHasFile() - Method in class net.sourceforge.seqware.common.model.WorkflowRun
-
Getter for the field isHasFile.
- getIsInvitationCode() - Method in class net.sourceforge.seqware.common.invitation.InvitationParams
-
Getter for the field isInvitationCode.
- getIsPublic() - Method in class io.seqware.webservice.generated.model.Sample
-
- getIsSelected() - Method in class net.sourceforge.seqware.common.model.Experiment
-
Getter for the field isSelected.
- getIsSelected() - Method in class net.sourceforge.seqware.common.model.File
-
Getter for the field isSelected.
- getIsSelected() - Method in class net.sourceforge.seqware.common.model.IUS
-
Getter for the field isSelected.
- getIsSelected() - Method in class net.sourceforge.seqware.common.model.Lane
-
Getter for the field isSelected.
- getIsSelected() - Method in class net.sourceforge.seqware.common.model.Processing
-
Getter for the field isSelected.
- getIsSelected() - Method in class net.sourceforge.seqware.common.model.Sample
-
Getter for the field
isSelected.
- getIsSelected() - Method in class net.sourceforge.seqware.common.model.Study
-
Getter for the field isSelected.
- getIsSelected() - Method in class net.sourceforge.seqware.common.model.WorkflowRun
-
Getter for the field isSelected.
- getIsStart() - Method in class net.sourceforge.solexatools.util.PageInfo
-
Getter for the field isStart.
- getIus() - Method in class net.sourceforge.seqware.common.model.FileReportRow
-
Getter for the field ius.
- getIus() - Method in class net.sourceforge.seqware.common.model.IUSAttribute
-
Getter for the field ius.
- getIus() - Method in class net.sourceforge.seqware.common.model.IUSLink
-
Getter for the field ius.
- getIus() - Method in class net.sourceforge.seqware.common.model.Lane
-
Getter for the field ius.
- getIUS() - Method in class net.sourceforge.seqware.common.model.Lane
-
getIUS.
- getIUS() - Method in class net.sourceforge.seqware.common.model.Processing
-
getIUS.
- getIus() - Method in class net.sourceforge.seqware.common.model.ProcessingIus
-
Getter for the field ius.
- getIUS() - Method in class net.sourceforge.seqware.common.model.Sample
-
getIUS.
- getIus() - Method in class net.sourceforge.seqware.common.model.SampleReportRow
-
Getter for the field ius.
- getIus() - Method in class net.sourceforge.seqware.common.model.SequencerRunReportId
-
Getter for the field ius.
- getIus() - Method in class net.sourceforge.seqware.common.model.WorkflowRun
-
Getter for the field ius.
- getIus() - Method in class net.sourceforge.solexatools.webapp.metamodel.SampleDetailsLineItem
-
Getter for the field ius.
- getIus() - Method in class net.sourceforge.solexatools.webapp.metamodel.StudySampleReportFileLineItem
-
Getter for the field ius.
- getIusAttributeCollection() - Method in class io.seqware.webservice.generated.model.Ius
-
- getIusAttributeId() - Method in class io.seqware.webservice.generated.model.IusAttribute
-
- getIusAttributeId() - Method in class net.sourceforge.seqware.common.model.IUSAttribute
-
Getter for the field iusAttributeId.
- getIusAttributes() - Method in class net.sourceforge.seqware.common.model.IUS
-
Getter for the field iusAttributes.
- getIusAttributes() - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.SampleInfo
-
Get the value of iusAttributes
- getIusCollection() - Method in class io.seqware.webservice.generated.model.Lane
-
- getIusCollection() - Method in class io.seqware.webservice.generated.model.Registration
-
- getIusCollection() - Method in class io.seqware.webservice.generated.model.Sample
-
- getIusDescription() - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.SampleInfo
-
Get the value of iusDescription
- getIusFiles() - Method in interface net.sourceforge.seqware.webservice.resources.tables.IusFilesResource
-
List files associated with Ius.
- getIusFiles() - Method in class net.sourceforge.seqware.webservice.resources.tables.IusFilesServerResource
-
List files associated with Ius.
- getIUSFrom(int) - Method in interface net.sourceforge.seqware.common.metadata.Metadata
-
Get IUSes (barcodes) from a lane or sample.
- getIUSFrom(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
-
- getIUSFrom(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection
-
- getIUSFrom(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS
-
- getIUSHtml(IUS, Registration, String, String, boolean, boolean, String) - Static method in class net.sourceforge.solexatools.util.NodeHtmlUtil
-
getIUSHtml.
- getIusId() - Method in class io.seqware.webservice.generated.model.FileReport
-
- getIusId() - Method in class io.seqware.webservice.generated.model.Ius
-
- getIusId() - Method in class io.seqware.webservice.generated.model.IusAttribute
-
- getIusId() - Method in class io.seqware.webservice.generated.model.IusLink
-
- getIusId() - Method in class io.seqware.webservice.generated.model.IusWorkflowRuns
-
- getIusId() - Method in class io.seqware.webservice.generated.model.ProcessingIus
-
- getIusId() - Method in class io.seqware.webservice.generated.model.SampleReport
-
- getIusId() - Method in class net.sourceforge.seqware.common.model.IUS
-
Getter for the field iusId.
- getIusLinkCollection() - Method in class io.seqware.webservice.generated.model.Ius
-
- getIusLinkId() - Method in class io.seqware.webservice.generated.model.IusLink
-
- getIusLinkId() - Method in class net.sourceforge.seqware.common.model.IUSLink
-
Getter for the field iusLinkId.
- getIusLinks() - Method in class net.sourceforge.seqware.common.model.IUS
-
Getter for the field iusLinks.
- getIusName() - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.SampleInfo
-
Get the value of iusName
- getIusService() - Method in class net.sourceforge.seqware.common.ContextImpl
-
Getter for the field iusService.
- getIusService() - Method in class net.sourceforge.solexatools.webapp.controller.BulkDownloadListDetailsController
-
Getter for the field iusService.
- getIUSService() - Method in class net.sourceforge.solexatools.webapp.controller.BulkDownloadListDetailsController
-
getIUSService.
- getIusService() - Method in class net.sourceforge.solexatools.webapp.controller.IUSController
-
Getter for the field iusService.
- getIUSService() - Method in class net.sourceforge.solexatools.webapp.controller.IUSController
-
getIUSService.
- getIusService() - Method in class net.sourceforge.solexatools.webapp.controller.IUSSetupController
-
Getter for the field iusService.
- getIusService() - Method in class net.sourceforge.solexatools.webapp.controller.LaneSampleAssociateController
-
Getter for the field iusService.
- getIUSService() - Method in class net.sourceforge.solexatools.webapp.controller.LaneSampleAssociateController
-
getIUSService.
- getIusService() - Method in class net.sourceforge.solexatools.webapp.controller.LaunchWorkflowListDetailsController
-
Getter for the field iusService.
- getIUSService() - Method in class net.sourceforge.solexatools.webapp.controller.LaunchWorkflowListDetailsController
-
getIUSService.
- getIusService() - Method in class net.sourceforge.solexatools.webapp.controller.SelectInputListController
-
Getter for the field iusService.
- getIUSService() - Method in class net.sourceforge.solexatools.webapp.controller.SelectInputListController
-
getIUSService.
- getIusService() - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunListDetailsController
-
Getter for the field iusService.
- getIUSService() - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunListDetailsController
-
getIUSService.
- getIusService() - Method in class net.sourceforge.solexatools.webapp.controller.StudyListDetailsController
-
Getter for the field iusService.
- getIUSService() - Method in class net.sourceforge.solexatools.webapp.controller.StudyListDetailsController
-
getIUSService.
- getIUSService() - Method in class net.sourceforge.solexatools.webapp.controller.StudyListDetailsFlatController
-
getIUSService.
- getIusService() - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileController
-
Getter for the field iusService.
- getIUSService() - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileController
-
getIUSService.
- getIusService() - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileSetupController
-
Getter for the field iusService.
- getIUSService() - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileSetupController
-
getIUSService.
- getIUSServiceBean() - Static method in class net.sourceforge.seqware.common.factory.BeanFactory
-
getIUSServiceBean.
- getIusSkip() - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.SampleInfo
-
Get the value of iusSkip
- getIusSwa() - Method in class net.sourceforge.seqware.common.hibernate.SequencerRunReport.Row
-
- getIusSwas() - Method in class net.sourceforge.seqware.common.business.impl.ValidationReportServiceImpl.ReportEntry
-
- getIusTag() - Method in class net.sourceforge.seqware.common.hibernate.SequencerRunReport.Row
-
- getIusWorkflowRunsCollection() - Method in class io.seqware.webservice.generated.model.Ius
-
- getIusWorkflowRunsCollection() - Method in class io.seqware.webservice.generated.model.WorkflowRun
-
- getIusWorkflowRunsId() - Method in class io.seqware.webservice.generated.model.IusWorkflowRuns
-
- getJobList() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.JobBatch
-
- getJobObject() - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object.OozieJob
-
- getJobObject() - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object.PegasusJob
-
- getJobs() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Workflow
-
get all jobs in current workflow
- getJobScript() - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object.OozieBashJob
-
- getJoinDevelopersMailingList() - Method in class net.sourceforge.seqware.common.model.Registration
-
Getter for the field joinDevelopersMailingList.
- getJoinUsersMailingList() - Method in class net.sourceforge.seqware.common.model.Registration
-
Getter for the field joinUsersMailingList.
- getJson(Representation) - Method in class net.sourceforge.seqware.webservice.resources.tables.FileChildLimitedWorkflowRunsResource
-
- getJsonEscapeAlgorithm() - Method in class net.sourceforge.seqware.common.model.Processing
-
getJsonEscapeAlgorithm.
- getJsonEscapeDefaultValue() - Method in class net.sourceforge.seqware.common.model.WorkflowParam
-
getJsonEscapeDefaultValue.
- getJsonEscapeDescription() - Method in class net.sourceforge.seqware.common.model.Experiment
-
getJsonEscapeDescription.
- getJsonEscapeDescription() - Method in class net.sourceforge.seqware.common.model.File
-
getJsonEscapeDescription.
- getJsonEscapeDescription() - Method in class net.sourceforge.seqware.common.model.IUS
-
getJsonEscapeDescription.
- getJsonEscapeDescription() - Method in class net.sourceforge.seqware.common.model.Lane
-
getJsonEscapeDescription.
- getJsonEscapeDescription() - Method in class net.sourceforge.seqware.common.model.Processing
-
getJsonEscapeDescription.
- getJsonEscapeDescription() - Method in class net.sourceforge.seqware.common.model.Sample
-
getJsonEscapeDescription.
- getJsonEscapeDescription() - Method in class net.sourceforge.seqware.common.model.SequencerRun
-
getJsonEscapeDescription.
- getJsonEscapeDescription() - Method in class net.sourceforge.seqware.common.model.Study
-
getJsonEscapeDescription.
- getJsonEscapeDescription() - Method in class net.sourceforge.seqware.common.model.Workflow
-
getJsonEscapeDescription.
- getJsonEscapeDescription200() - Method in class net.sourceforge.seqware.common.model.Experiment
-
getJsonEscapeDescription200.
- getJsonEscapeDescription200() - Method in class net.sourceforge.seqware.common.model.Study
-
getJsonEscapeDescription200.
- getJsonEscapeDisplayName() - Method in class net.sourceforge.seqware.common.model.WorkflowParam
-
getJsonEscapeDisplayName.
- getJsonEscapeDisplayName() - Method in class net.sourceforge.seqware.common.model.WorkflowParamValue
-
getJsonEscapeDisplayName.
- getJsonEscapeFileName() - Method in class net.sourceforge.seqware.common.model.File
-
getJsonEscapeFileName.
- getJsonEscapeFullName() - Method in class net.sourceforge.seqware.common.model.Workflow
-
getJsonEscapeFullName.
- getJsonEscapeKey() - Method in class net.sourceforge.seqware.common.model.WorkflowParam
-
getJsonEscapeKey.
- getJsonEscapeName() - Method in class net.sourceforge.seqware.common.model.Experiment
-
getJsonEscapeName.
- getJsonEscapeName() - Method in class net.sourceforge.seqware.common.model.IUS
-
getJsonEscapeName.
- getJsonEscapeName() - Method in class net.sourceforge.seqware.common.model.Lane
-
getJsonEscapeName.
- getJsonEscapeName() - Method in class net.sourceforge.seqware.common.model.Sample
-
getJsonEscapeName.
- getJsonEscapeName() - Method in class net.sourceforge.seqware.common.model.SequencerRun
-
getJsonEscapeName.
- getJsonEscapeName() - Method in class net.sourceforge.seqware.common.model.Workflow
-
getJsonEscapeName.
- getJsonEscapeName() - Method in class net.sourceforge.seqware.common.model.WorkflowRun
-
getJsonEscapeName.
- getJsonEscapeTitle() - Method in class net.sourceforge.seqware.common.model.Experiment
-
getJsonEscapeTitle.
- getJsonEscapeTitle() - Method in class net.sourceforge.seqware.common.model.Sample
-
getJsonEscapeTitle.
- getJsonEscapeTitle() - Method in class net.sourceforge.seqware.common.model.Study
-
getJsonEscapeTitle.
- getJsonEscapeType() - Method in class net.sourceforge.seqware.common.model.WorkflowParam
-
getJsonEscapeType.
- getJsonEscapeValue() - Method in class net.sourceforge.seqware.common.model.WorkflowParam
-
getJsonEscapeValue.
- getJsonEscapeValue() - Method in class net.sourceforge.seqware.common.model.WorkflowParamValue
-
getJsonEscapeValue.
- getKey() - Method in class io.seqware.webservice.generated.model.WorkflowParam
-
- getKey() - Method in class io.seqware.webservice.generated.model.WorkflowRunParam
-
- getKey() - Method in class net.sourceforge.seqware.common.model.WorkflowParam
-
Getter for the field key.
- getKey() - Method in class net.sourceforge.seqware.common.model.WorkflowRunParam
-
Getter for the field key.
- getKey() - Method in enum net.sourceforge.seqware.common.util.maptools.ReservedIniKeys
-
- getKey() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Argument
-
Getter for the field key.
- getKey() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.JobProfile
-
Getter for the field key.
- getKeyValueFromFile(String) - Static method in class net.sourceforge.seqware.common.util.filetools.FileTools
-
getKeyValueFromFile.
- getLabel() - Method in class io.seqware.webservice.generated.model.ExperimentLink
-
- getLabel() - Method in class io.seqware.webservice.generated.model.IusLink
-
- getLabel() - Method in class io.seqware.webservice.generated.model.LaneLink
-
- getLabel() - Method in class io.seqware.webservice.generated.model.ProcessingExperiments
-
- getLabel() - Method in class io.seqware.webservice.generated.model.ProcessingIus
-
- getLabel() - Method in class io.seqware.webservice.generated.model.ProcessingLanes
-
- getLabel() - Method in class io.seqware.webservice.generated.model.ProcessingSamples
-
- getLabel() - Method in class io.seqware.webservice.generated.model.ProcessingSequencerRuns
-
- getLabel() - Method in class io.seqware.webservice.generated.model.ProcessingStudies
-
- getLabel() - Method in class io.seqware.webservice.generated.model.SampleLink
-
- getLabel() - Method in class io.seqware.webservice.generated.model.StudyLink
-
- getLabel() - Method in class net.sourceforge.seqware.common.model.ExperimentLink
-
Getter for the field label.
- getLabel() - Method in class net.sourceforge.seqware.common.model.IUSLink
-
Getter for the field label.
- getLabel() - Method in class net.sourceforge.seqware.common.model.LaneLink
-
Getter for the field label.
- getLabel() - Method in class net.sourceforge.seqware.common.model.ProcessingExperiments
-
Getter for the field label.
- getLabel() - Method in class net.sourceforge.seqware.common.model.ProcessingIus
-
Getter for the field label.
- getLabel() - Method in class net.sourceforge.seqware.common.model.ProcessingLanes
-
Getter for the field label.
- getLabel() - Method in class net.sourceforge.seqware.common.model.ProcessingSamples
-
Getter for the field label.
- getLabel() - Method in class net.sourceforge.seqware.common.model.ProcessingSequencerRuns
-
Getter for the field label.
- getLabel() - Method in class net.sourceforge.seqware.common.model.ProcessingStudies
-
Getter for the field label.
- getLabel() - Method in class net.sourceforge.seqware.common.model.SampleLink
-
Getter for the field label.
- getLabel() - Method in class net.sourceforge.seqware.common.model.StudyLink
-
Getter for the field label.
- getLane(int) - Method in interface net.sourceforge.seqware.common.metadata.Metadata
-
getLane.
- getLane(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
-
- getLane(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection
-
- getLane(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS
-
- getLane() - Method in class net.sourceforge.seqware.common.model.FileReportRow
-
Getter for the field lane.
- getLane() - Method in class net.sourceforge.seqware.common.model.IUS
-
Getter for the field lane.
- getLane() - Method in class net.sourceforge.seqware.common.model.LaneAttribute
-
Getter for the field lane.
- getLane() - Method in class net.sourceforge.seqware.common.model.LaneLink
-
Getter for the field lane.
- getLane() - Method in class net.sourceforge.seqware.common.model.ProcessingLanes
-
Getter for the field lane.
- getLane() - Method in class net.sourceforge.seqware.common.model.SampleReportRow
-
Getter for the field lane.
- getLane() - Method in class net.sourceforge.seqware.common.model.SequencerRunReportId
-
Getter for the field lane.
- getLane() - Method in class net.sourceforge.seqware.common.model.ShareLane
-
Getter for the field lane.
- getLane() - Method in class net.sourceforge.seqware.pipeline.plugins.filelinker.FileLinkerLine
-
- getLane() - Method in class net.sourceforge.solexatools.webapp.metamodel.SampleDetailsLineItem
-
Getter for the field lane.
- getLane1() - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
-
Getter for the field lane1.
- getLane2() - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
-
Getter for the field lane2.
- getLane3() - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
-
Getter for the field lane3.
- getLane4() - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
-
Getter for the field lane4.
- getLane5() - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
-
Getter for the field lane5.
- getLane6() - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
-
Getter for the field lane6.
- getLane7() - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
-
Getter for the field lane7.
- getLane8() - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
-
Getter for the field lane8.
- getLane_url() - Method in class net.sourceforge.seqware.webservice.dto.IusDto
-
Getter for the field lane_url.
- getLaneAttributeCollection() - Method in class io.seqware.webservice.generated.model.Lane
-
- getLaneAttributeId() - Method in class io.seqware.webservice.generated.model.LaneAttribute
-
- getLaneAttributeId() - Method in class net.sourceforge.seqware.common.model.LaneAttribute
-
Getter for the field laneAttributeId.
- getLaneAttributes() - Method in class net.sourceforge.seqware.common.model.Lane
-
Getter for the field laneAttributes.
- getLaneAttributes() - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.LaneInfo
-
- getLaneCollection() - Method in class io.seqware.webservice.generated.model.LaneType
-
- getLaneCollection() - Method in class io.seqware.webservice.generated.model.LibrarySelection
-
- getLaneCollection() - Method in class io.seqware.webservice.generated.model.LibrarySource
-
- getLaneCollection() - Method in class io.seqware.webservice.generated.model.LibraryStrategy
-
- getLaneCollection() - Method in class io.seqware.webservice.generated.model.Organism
-
- getLaneCollection() - Method in class io.seqware.webservice.generated.model.Registration
-
- getLaneCollection() - Method in class io.seqware.webservice.generated.model.Sample
-
- getLaneCollection() - Method in class io.seqware.webservice.generated.model.SequencerRun
-
- getLaneCollection() - Method in class io.seqware.webservice.generated.model.StudyType
-
- getLaneCount() - Method in class net.sourceforge.seqware.common.model.SequencerRunWizardDTO
-
Getter for the field laneCount.
- getLaneCycleDescriptor() - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.LaneInfo
-
Get the value of laneCycleDescriptor
- getLaneDescription() - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.LaneInfo
-
Get the value of laneDescription
- getLaneHtml(Lane, Registration, String, String, String) - Static method in class net.sourceforge.solexatools.util.NodeHtmlUtil
-
getLaneHtml.
- getLaneHtml(Lane, Registration, Integer) - Static method in class net.sourceforge.solexatools.util.TreeNodeHtmlUtil
-
getLaneHtml.
- getLaneId() - Method in class io.seqware.webservice.generated.model.FileReport
-
- getLaneId() - Method in class io.seqware.webservice.generated.model.Ius
-
- getLaneId() - Method in class io.seqware.webservice.generated.model.Lane
-
- getLaneId() - Method in class io.seqware.webservice.generated.model.LaneAttribute
-
- getLaneId() - Method in class io.seqware.webservice.generated.model.LaneLink
-
- getLaneId() - Method in class io.seqware.webservice.generated.model.LaneWorkflowRuns
-
- getLaneId() - Method in class io.seqware.webservice.generated.model.ProcessingLanes
-
- getLaneId() - Method in class io.seqware.webservice.generated.model.SampleReport
-
- getLaneId() - Method in class io.seqware.webservice.generated.model.ShareLane
-
- getLaneId() - Method in class net.sourceforge.seqware.common.model.Lane
-
Getter for the field laneId.
- getLaneIndex() - Method in class io.seqware.webservice.generated.model.Lane
-
- getLaneIndex() - Method in class net.sourceforge.seqware.common.model.Lane
-
Getter for the field laneIndex.
- getLaneLinkCollection() - Method in class io.seqware.webservice.generated.model.Lane
-
- getLaneLinkId() - Method in class io.seqware.webservice.generated.model.LaneLink
-
- getLaneLinkId() - Method in class net.sourceforge.seqware.common.model.LaneLink
-
Getter for the field laneLinkId.
- getLaneLinks() - Method in class net.sourceforge.seqware.common.model.Lane
-
Getter for the field laneLinks.
- getLaneName() - Method in class net.sourceforge.seqware.common.hibernate.SequencerRunReport.Row
-
- getLaneName() - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.LaneInfo
-
Get the value of laneName
- getLaneNumber() - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.LaneInfo
-
Get the value of laneNumber
- getLanes() - Method in class net.sourceforge.seqware.common.model.Processing
-
Getter for the field lanes.
- getLanes() - Method in class net.sourceforge.seqware.common.model.Sample
-
Getter for the field
lanes.
- getLanes() - Method in class net.sourceforge.seqware.common.model.SequencerRun
-
Getter for the field lanes.
- getLanes() - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
-
Getter for the field lanes.
- getLanes() - Method in class net.sourceforge.seqware.common.model.WorkflowRun
-
Getter for the field lanes.
- getLanes() - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.RunInfo
-
Get the value of lanes
- getLaneService() - Method in class net.sourceforge.seqware.common.ContextImpl
-
Getter for the field laneService.
- getLaneService() - Method in class net.sourceforge.solexatools.validation.LaneValidator
-
Getter for the field laneService.
- getLaneService() - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysBulkDownloadListDetailsController
-
Getter for the field laneService.
- getLaneService() - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysListDetailsController
-
Getter for the field laneService.
- getLaneService() - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysRunningListDetailsController
-
Getter for the field laneService.
- getLaneService() - Method in class net.sourceforge.solexatools.webapp.controller.BulkDownloadListDetailsController
-
Getter for the field laneService.
- getLaneService() - Method in class net.sourceforge.solexatools.webapp.controller.DownloadFileListController
-
Getter for the field laneService.
- getLaneService() - Method in class net.sourceforge.solexatools.webapp.controller.LaneController
-
Getter for the field laneService.
- getLaneService() - Method in class net.sourceforge.solexatools.webapp.controller.LaneSampleAssociateController
-
Getter for the field laneService.
- getLaneService() - Method in class net.sourceforge.solexatools.webapp.controller.LaneSampleAssociateSetupController
-
Getter for the field laneService.
- getLaneService() - Method in class net.sourceforge.solexatools.webapp.controller.LaneSetupController
-
Getter for the field laneService.
- getLaneService() - Method in class net.sourceforge.solexatools.webapp.controller.LaunchWorkflowListDetailsController
-
Getter for the field laneService.
- getLaneService() - Method in class net.sourceforge.solexatools.webapp.controller.SampleSetupController
-
Getter for the field laneService.
- getLaneService() - Method in class net.sourceforge.solexatools.webapp.controller.SaveOpenNodeController
-
Getter for the field laneService.
- getLaneService() - Method in class net.sourceforge.solexatools.webapp.controller.SelectInputListController
-
Getter for the field laneService.
- getLaneService() - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunController
-
Getter for the field laneService.
- getLaneService() - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunControllerDTO
-
Getter for the field laneService.
- getLaneService() - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunListDetailsController
-
Getter for the field laneService.
- getLaneService() - Method in class net.sourceforge.solexatools.webapp.controller.StudyListDetailsController
-
Getter for the field laneService.
- getLaneService() - Method in class net.sourceforge.solexatools.webapp.controller.StudyListDetailsFlatController
-
Getter for the field laneService.
- getLaneService() - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileController
-
Getter for the field laneService.
- getLaneService() - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileSetupController
-
Getter for the field laneService.
- getLaneService() - Method in class net.sourceforge.solexatools.webapp.controller.UploadSequenceController
-
Getter for the field laneService.
- getLaneServiceBean() - Static method in class net.sourceforge.seqware.common.factory.BeanFactory
-
getLaneServiceBean.
- getLanesFrom(int) - Method in interface net.sourceforge.seqware.common.metadata.Metadata
-
Get Lanes from a sequencer run.
- getLanesFrom(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
-
- getLanesFrom(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection
-
- getLanesFrom(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS
-
- getLaneSkip() - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.LaneInfo
-
Get the value of laneSkip
- getLaneSwa() - Method in class net.sourceforge.seqware.common.hibernate.SequencerRunReport.Row
-
- getLaneSwas() - Method in class net.sourceforge.seqware.common.business.impl.ValidationReportServiceImpl.ReportEntry
-
- getLaneTypeId() - Method in class io.seqware.webservice.generated.model.LaneType
-
- getLaneWorkflowRunsCollection() - Method in class io.seqware.webservice.generated.model.Lane
-
- getLaneWorkflowRunsCollection() - Method in class io.seqware.webservice.generated.model.WorkflowRun
-
- getLaneWorkflowRunsId() - Method in class io.seqware.webservice.generated.model.LaneWorkflowRuns
-
- getLastName() - Method in class io.seqware.webservice.generated.model.Registration
-
- getLastName() - Method in class net.sourceforge.seqware.common.model.Registration
-
Getter for the field lastName.
- getLastName() - Method in class net.sourceforge.seqware.webservice.dto.OwnerDto
-
Getter for the field lastName.
- getLastUpdateTstmp() - Method in class io.seqware.webservice.generated.model.Registration
-
- getLayout() - Method in class io.seqware.webservice.generated.model.ExperimentLibraryDesign
-
- getLayout() - Method in class net.sourceforge.seqware.common.model.ExperimentLibraryDesign
-
Getter for the field layout.
- getLength() - Method in class io.seqware.webservice.generated.model.ExperimentSpotDesignReadSpec
-
- getLength() - Method in class net.sourceforge.seqware.common.model.ExperimentSpotDesignReadSpec
-
Getter for the field length.
- getLibraries() - Method in class net.sourceforge.seqware.common.business.impl.LibraryServiceImpl
-
Returns a complete list of libraries.
- getLibraries(Map<String, String>) - Method in class net.sourceforge.seqware.common.business.impl.LibraryServiceImpl
-
Returns a list of libraries that match all attributes provided in the give
attributes Map.
- getLibraries() - Method in interface net.sourceforge.seqware.common.business.LibraryService
-
Returns a complete list of libraries.
- getLibraries(Map<String, String>) - Method in interface net.sourceforge.seqware.common.business.LibraryService
-
Returns a list of libraries that match all attributes provided in the give
attributes Map.
- getLibraries(String, String) - Method in class net.sourceforge.seqware.common.dao.hibernate.LibraryDAOHibernate
-
Returns list of libraries that contain the attribute
attributeName=attributeValue.
- getLibraries() - Method in class net.sourceforge.seqware.common.dao.hibernate.LibraryDAOHibernate
-
Returns a complete list of libraries.
- getLibraries(String, String) - Method in interface net.sourceforge.seqware.common.dao.LibraryDAO
-
Returns list of libraries that contain the attribute
attributeName=attributeValue.
- getLibraries() - Method in interface net.sourceforge.seqware.common.dao.LibraryDAO
-
Returns a complete list of libraries.
- getLibraries() - Method in class net.sourceforge.seqware.webservice.resources.tables.LibrariesResource
-
getLibraries.
- getLibraryId() - Method in class net.sourceforge.seqware.webservice.dto.LibraryIdentityDto
-
Getter for the field libraryId.
- getLibrarySamples() - Method in class net.sourceforge.seqware.common.hibernate.reports.WorkflowRunReportRow
-
Getter for the field librarySamples.
- getLibrarySelection() - Method in class io.seqware.webservice.generated.model.Lane
-
- getLibrarySelection() - Method in class net.sourceforge.seqware.common.model.Lane
-
- getLibrarySelectionAcc() - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.LaneInfo
-
Get the value of librarySelectionAcc
- getLibrarySelectionId() - Method in class io.seqware.webservice.generated.model.LibrarySelection
-
- getLibrarySelectionId() - Method in class net.sourceforge.seqware.common.model.LibrarySelection
-
Getter for the field librarySelectionId.
- getLibrarySelections() - Method in interface net.sourceforge.seqware.common.metadata.Metadata
-
getLibrarySelections.
- getLibrarySelections() - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
-
- getLibrarySelections() - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection
-
- getLibrarySelections() - Method in class net.sourceforge.seqware.common.metadata.MetadataWS
-
- getLibrarySelectionService() - Method in class net.sourceforge.seqware.common.ContextImpl
-
- getLibrarySelectionService() - Method in class net.sourceforge.solexatools.webapp.controller.ExperimentController
-
Getter for the field librarySelectionService.
- getLibrarySelectionService() - Method in class net.sourceforge.solexatools.webapp.controller.ExperimentSetupController
-
Getter for the field librarySelectionService.
- getLibrarySelectionServiceBean() - Static method in class net.sourceforge.seqware.common.factory.BeanFactory
-
getLibrarySelectionServiceBean.
- getLibraryService() - Method in class net.sourceforge.seqware.common.ContextImpl
-
Getter for the field libraryService.
- getLibraryServiceBean() - Static method in class net.sourceforge.seqware.common.factory.BeanFactory
-
getLibraryServiceBean.
- getLibrarySizeCode() - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.SampleInfo
-
- getLibrarySource() - Method in class io.seqware.webservice.generated.model.Lane
-
- getLibrarySource() - Method in interface net.sourceforge.seqware.common.metadata.Metadata
-
getLibrarySource.
- getLibrarySource() - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
-
- getLibrarySource() - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection
-
- getLibrarySource() - Method in class net.sourceforge.seqware.common.metadata.MetadataWS
-
- getLibrarySource() - Method in class net.sourceforge.seqware.common.model.Lane
-
- getLibrarySourceAcc() - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.LaneInfo
-
Get the value of librarySourceAcc
- getLibrarySourceId() - Method in class io.seqware.webservice.generated.model.LibrarySource
-
- getLibrarySourceId() - Method in class net.sourceforge.seqware.common.model.LibrarySource
-
Getter for the field librarySourceId.
- getLibrarySourceService() - Method in class net.sourceforge.seqware.common.ContextImpl
-
- getLibrarySourceService() - Method in class net.sourceforge.solexatools.webapp.controller.ExperimentController
-
Getter for the field librarySourceService.
- getLibrarySourceService() - Method in class net.sourceforge.solexatools.webapp.controller.ExperimentSetupController
-
Getter for the field librarySourceService.
- getLibrarySourceServiceBean() - Static method in class net.sourceforge.seqware.common.factory.BeanFactory
-
getLibrarySourceServiceBean.
- getLibrarySourceTemplateType() - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.SampleInfo
-
Get the value of librarySourceTemplateType
- getLibraryStrategies() - Method in interface net.sourceforge.seqware.common.metadata.Metadata
-
getLibraryStrategies.
- getLibraryStrategies() - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
-
- getLibraryStrategies() - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection
-
- getLibraryStrategies() - Method in class net.sourceforge.seqware.common.metadata.MetadataWS
-
- getLibraryStrategy() - Method in class io.seqware.webservice.generated.model.Lane
-
- getLibraryStrategy() - Method in class net.sourceforge.seqware.common.model.Lane
-
- getLibraryStrategyAcc() - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.LaneInfo
-
Get the value of libraryStrategyAcc
- getLibraryStrategyId() - Method in class io.seqware.webservice.generated.model.LibraryStrategy
-
- getLibraryStrategyId() - Method in class net.sourceforge.seqware.common.model.LibraryStrategy
-
Getter for the field libraryStrategyId.
- getLibraryStrategyService() - Method in class net.sourceforge.seqware.common.ContextImpl
-
- getLibraryStrategyService() - Method in class net.sourceforge.solexatools.webapp.controller.ExperimentController
-
Getter for the field libraryStrategyService.
- getLibraryStrategyService() - Method in class net.sourceforge.solexatools.webapp.controller.ExperimentSetupController
-
Getter for the field libraryStrategyService.
- getLibraryStrategyServiceBean() - Static method in class net.sourceforge.seqware.common.factory.BeanFactory
-
getLibraryStrategyServiceBean.
- getLibraryType() - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.SampleInfo
-
- getLibraryType() - Method in class net.sourceforge.solexatools.webapp.metamodel.StudySampleReportFileLineItem
-
Getter for the field libraryType.
- getLimsAdmin() - Method in class io.seqware.webservice.generated.model.Registration
-
- getList() - Method in class net.sourceforge.seqware.common.model.lists.ExperimentLibraryDesignList
-
getList.
- getList() - Method in class net.sourceforge.seqware.common.model.lists.ExperimentList
-
getList.
- getList() - Method in class net.sourceforge.seqware.common.model.lists.ExperimentSpotDesignList
-
getList.
- getList() - Method in class net.sourceforge.seqware.common.model.lists.ExperimentSpotDesignReadSpecList
-
getList.
- getList() - Method in class net.sourceforge.seqware.common.model.lists.FileList
-
getList.
- getList() - Method in class net.sourceforge.seqware.common.model.lists.IntegerList
-
getList.
- getList() - Method in class net.sourceforge.seqware.common.model.lists.IUSList
-
getList.
- getList() - Method in class net.sourceforge.seqware.common.model.lists.LaneList
-
getList.
- getList() - Method in class net.sourceforge.seqware.common.model.lists.LibrarySelectionList
-
getList.
- getList() - Method in class net.sourceforge.seqware.common.model.lists.LibrarySourceList
-
getList.
- getList() - Method in class net.sourceforge.seqware.common.model.lists.LibraryStrategyList
-
getList.
- getList() - Method in class net.sourceforge.seqware.common.model.lists.OrganismList
-
getList.
- getList() - Method in class net.sourceforge.seqware.common.model.lists.PlatformList
-
getList.
- getList() - Method in class net.sourceforge.seqware.common.model.lists.ProcessingList
-
getList.
- getList() - Method in class net.sourceforge.seqware.common.model.lists.ReturnValueList
-
getList.
- getList() - Method in class net.sourceforge.seqware.common.model.lists.SampleList
-
getList.
- getList() - Method in class net.sourceforge.seqware.common.model.lists.SequencerRunList
-
getList.
- getList() - Method in class net.sourceforge.seqware.common.model.lists.StudyList
-
getList.
- getList() - Method in class net.sourceforge.seqware.common.model.lists.StudyTypeList
-
getList.
- getList() - Method in class net.sourceforge.seqware.common.model.lists.WorkflowList
-
getList.
- getList() - Method in class net.sourceforge.seqware.common.model.lists.WorkflowParamList
-
getList.
- getList() - Method in class net.sourceforge.seqware.common.model.lists.WorkflowParamValueList
-
getList.
- getList() - Method in class net.sourceforge.seqware.common.model.lists.WorkflowRunList
-
getList.
- getList() - Method in class net.sourceforge.seqware.common.model.lists.WorkflowRunList2
-
getList.
- getLocalhost(OptionSet) - Static method in class net.sourceforge.seqware.common.util.filetools.FileTools
-
Get the localhost and a return value describing the failure condition
if we are unable to get the localhost
- getLocalhost() - Static method in class net.sourceforge.seqware.pipeline.plugins.ITUtility
-
- getLock() - Method in class net.sourceforge.seqware.common.util.filetools.lock.SimpleFileLock
-
Deprecated.
Lock file, do not clear on exit
- getLock(boolean) - Method in class net.sourceforge.seqware.common.util.filetools.lock.SimpleFileLock
-
Deprecated.
Lock file, but give option to free lock when the JVM exits.
- getLock(int, int) - Method in class net.sourceforge.seqware.common.util.filetools.lock.SimpleFileLock
-
Deprecated.
getLock.
- getLongName() - Method in class net.sourceforge.seqware.common.model.Platform
-
getLongName.
- getLookupToken() - Method in class net.sourceforge.seqware.pipeline.workflowV2.AbstractWorkflowEngine
-
An engine-specific token for this workflow run that can be used to lookup
relevant runtime data.
- getLookupToken() - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.OozieWorkflowEngine
-
- getLookupToken() - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.PegasusWorkflowEngine
-
- getMainClass() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.AbstractJob
-
return the main class for a Java job, or the script.pl for a perl Job
- getMapred_job_tracker() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Environment
-
- getMaxMemory() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.AbstractJob
-
- getMaxMemory() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Command
-
- getMaxMemory() - Method in interface net.sourceforge.seqware.pipeline.workflowV2.model.Job
-
- getMd5sum() - Method in class io.seqware.webservice.generated.model.File
-
- getMd5sum() - Method in class net.sourceforge.seqware.common.model.File
-
Getter for the field md5sum.
- getMd5sum() - Method in class net.sourceforge.seqware.common.module.FileMetadata
-
- getMd5sum() - Method in class net.sourceforge.seqware.pipeline.plugins.filelinker.FileLinkerLine
-
- getMd5sum() - Method in class net.sourceforge.seqware.webservice.dto.FileDto
-
Getter for the field md5sum.
- getMeaning() - Method in enum net.sourceforge.seqware.common.module.ReturnValue.ExitStatus
-
- getMemory() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Environment
-
- getMemReq() - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowInfo
-
Getter for the field memReq.
- getMetadata() - Method in class net.sourceforge.seqware.pipeline.bundle.Bundle
-
Getter for the field metadata.
- getMetadata() - Method in class net.sourceforge.seqware.pipeline.module.Module
-
Getter for the field metadata.
- getMetadata() - Method in class net.sourceforge.seqware.pipeline.plugins.WorkflowStatusChecker
-
- getMetadata() - Method in class net.sourceforge.seqware.queryengine.webservice.model.MetadataDB
-
getMetadata.
- getMetadata(long) - Method in class net.sourceforge.seqware.queryengine.webservice.model.MetadataDB
-
getMetadata.
- getMetadata_output_dir() - Method in class net.sourceforge.seqware.pipeline.workflowV2.AbstractWorkflowDataModel
-
- getMetadata_output_file_prefix() - Method in class net.sourceforge.seqware.pipeline.workflowV2.AbstractWorkflowDataModel
-
- getMetadataOutputPrefix() - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object.OozieProvisionFileJob
-
- getMetadataOutputPrefix() - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object.ProvisionFilesJob
-
- getMetadataWriteback() - Method in class net.sourceforge.seqware.pipeline.deciders.BasicDecider
-
- getMetaType() - Method in class io.seqware.webservice.generated.model.File
-
- getMetaType() - Method in class io.seqware.webservice.generated.model.FileType
-
- getMetaType() - Method in class net.sourceforge.seqware.common.model.File
-
Getter for the field metaType.
- getMetaType() - Method in class net.sourceforge.seqware.common.model.FileType
-
Getter for the field metaType.
- getMetaType() - Method in class net.sourceforge.seqware.common.module.FileMetadata
-
- getMetaType() - Method in class net.sourceforge.seqware.pipeline.deciders.BasicDecider
-
- getMetaType() - Method in class net.sourceforge.seqware.webservice.dto.FileDto
-
Getter for the field metaType.
- getMimeType() - Method in class net.sourceforge.seqware.pipeline.plugins.filelinker.FileLinkerLine
-
- getModelAndView(String, ModelAndView) - Static method in class net.sourceforge.solexatools.util.StudyBuildTree
-
getModelAndView.
- getModelId() - Method in class net.sourceforge.seqware.common.model.ExperimentLibraryDesign
-
- getModelId() - Method in class net.sourceforge.seqware.common.model.ExperimentSpotDesign
-
- getModelId() - Method in class net.sourceforge.seqware.common.model.ExperimentSpotDesignReadSpec
-
- getModelId() - Method in class net.sourceforge.seqware.common.model.LibrarySelection
-
- getModelId() - Method in class net.sourceforge.seqware.common.model.LibrarySource
-
- getModelId() - Method in class net.sourceforge.seqware.common.model.LibraryStrategy
-
- getModelId() - Method in class net.sourceforge.seqware.common.model.Organism
-
- getModelId() - Method in class net.sourceforge.seqware.common.model.Platform
-
- getModelId() - Method in interface net.sourceforge.seqware.common.model.SecondTierModel
-
Get the id for this model
- getModelId() - Method in class net.sourceforge.seqware.common.model.StudyType
-
- getModuleType() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.JobModule
-
Getter for the field moduleType.
- getName() - Method in class io.seqware.webservice.generated.model.Experiment
-
- getName() - Method in class io.seqware.webservice.generated.model.ExperimentLibraryDesign
-
- getName() - Method in class io.seqware.webservice.generated.model.Ius
-
- getName() - Method in class io.seqware.webservice.generated.model.Lane
-
- getName() - Method in class io.seqware.webservice.generated.model.LaneType
-
- getName() - Method in class io.seqware.webservice.generated.model.LibrarySelection
-
- getName() - Method in class io.seqware.webservice.generated.model.LibrarySource
-
- getName() - Method in class io.seqware.webservice.generated.model.LibraryStrategy
-
- getName() - Method in class io.seqware.webservice.generated.model.Organism
-
- getName() - Method in class io.seqware.webservice.generated.model.Platform
-
- getName() - Method in class io.seqware.webservice.generated.model.Sample
-
- getName() - Method in class io.seqware.webservice.generated.model.SequencerRun
-
- getName() - Method in class io.seqware.webservice.generated.model.StudyType
-
- getName() - Method in class io.seqware.webservice.generated.model.Workflow
-
- getName() - Method in class io.seqware.webservice.generated.model.WorkflowRun
-
- getName() - Method in class net.sourceforge.seqware.common.model.Experiment
-
Getter for the field name.
- getName() - Method in class net.sourceforge.seqware.common.model.ExperimentLibraryDesign
-
Getter for the field name.
- getName() - Method in class net.sourceforge.seqware.common.model.IUS
-
Getter for the field name.
- getName() - Method in class net.sourceforge.seqware.common.model.Lane
-
Getter for the field name.
- getName() - Method in class net.sourceforge.seqware.common.model.LibrarySelection
-
Getter for the field name.
- getName() - Method in class net.sourceforge.seqware.common.model.LibrarySource
-
Getter for the field name.
- getName() - Method in class net.sourceforge.seqware.common.model.LibraryStrategy
-
Getter for the field name.
- getName() - Method in class net.sourceforge.seqware.common.model.Organism
-
Getter for the field name.
- getName() - Method in class net.sourceforge.seqware.common.model.Platform
-
Getter for the field name.
- getName() - Method in class net.sourceforge.seqware.common.model.Sample
-
Getter for the field
name.
- getName() - Method in class net.sourceforge.seqware.common.model.SequencerRun
-
Getter for the field name.
- getName() - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
-
Getter for the field name.
- getName() - Method in class net.sourceforge.seqware.common.model.StudyType
-
Getter for the field name.
- getName() - Method in class net.sourceforge.seqware.common.model.Workflow
-
Getter for the field name.
- getName() - Method in class net.sourceforge.seqware.common.model.WorkflowRun
-
Getter for the field name.
- getName() - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowInfo
-
Getter for the field name.
- getName() - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.SampleInfo
-
Get the value of name
- getName() - Method in class net.sourceforge.seqware.pipeline.workflowV2.AbstractWorkflowDataModel
-
- getName() - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object.OozieJob
-
- getName() - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object.WorkflowExecutable
-
- getName() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.JobModule
-
getName.
- getName() - Method in enum net.sourceforge.seqware.pipeline.workflowV2.model.Module
-
getName.
- getName() - Method in class net.sourceforge.seqware.webservice.dto.AttributeDto
-
Getter for the field name.
- getName() - Method in class net.sourceforge.seqware.webservice.dto.LibraryDto
-
Getter for the field name.
- getName() - Method in class net.sourceforge.seqware.webservice.dto.OrganismDto
-
Getter for the field name.
- getName() - Method in class net.sourceforge.solexatools.webapp.metamodel.Flexigrid.ColumnModel
-
- getNameNode() - Method in class net.sourceforge.seqware.common.business.UploadFile
-
Getter for the field nameNode.
- getNamespace() - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object.WorkflowExecutable
-
- getNamespace() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.JobProfile
-
getNamespace.
- getNamespace() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Requirement
-
- getNcbiTaxid() - Method in class io.seqware.webservice.generated.model.Organism
-
- getNcbiTaxId() - Method in class net.sourceforge.seqware.common.model.Organism
-
Getter for the field ncbiTaxId.
- getNcbiTaxonomyId() - Method in class net.sourceforge.seqware.webservice.dto.OrganismDto
-
Getter for the field ncbiTaxonomyId.
- getNetwork() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Environment
-
- getNetworkReq() - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowInfo
-
Getter for the field networkReq.
- getNewType() - Method in class io.seqware.webservice.generated.model.Study
-
- getNewType() - Method in class net.sourceforge.seqware.common.model.Study
-
Getter for the field newType.
- getNodeHtml(Processing, Registration, String, boolean, boolean, boolean, boolean, boolean, String) - Static method in class net.sourceforge.solexatools.util.NodeHtmlUtil
-
getNodeHtml.
- getNodeHtml(Processing, Registration) - Static method in class net.sourceforge.solexatools.util.TreeNodeHtmlUtil
-
getNodeHtml.
- getNodeIds(Object) - Static method in class net.sourceforge.solexatools.util.FindChildUtil
-
getNodeIds.
- getNominalLength() - Method in class io.seqware.webservice.generated.model.ExperimentLibraryDesign
-
- getNominalLength() - Method in class net.sourceforge.seqware.common.model.ExperimentLibraryDesign
-
Getter for the field nominalLength.
- getNominalSdev() - Method in class io.seqware.webservice.generated.model.ExperimentLibraryDesign
-
- getNominalSdev() - Method in class net.sourceforge.seqware.common.model.ExperimentLibraryDesign
-
Getter for the field nominalSdev.
- getNoOp() - Static method in class net.sourceforge.seqware.common.metadata.MetadataFactory
-
- getNotes() - Method in class io.seqware.webservice.generated.model.Invoice
-
- getNotes() - Method in class net.sourceforge.seqware.common.model.Invoice
-
Getter for the field notes.
- getNotRunned() - Method in class net.sourceforge.solexatools.webapp.metamodel.StudySampleReportLineItem
-
Getter for the field notRunned.
- getOffspringProcessings() - Method in class net.sourceforge.seqware.common.model.WorkflowRun
-
Getter for the field offspringProcessings.
- getOkTo() - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object.OozieJob
-
- getOOZIE_APP_PATH() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Environment
-
- getOOZIE_APP_ROOT() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Environment
-
- getOOZIE_JOBTRACKER() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Environment
-
- getOOZIE_NAMENODE() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Environment
-
- getOOZIE_QUEUENAME() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Environment
-
- getOOZIE_URL() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Environment
-
- getOOZIE_WORK_DIR() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Environment
-
- getOozieWorkingDir() - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object.OozieJob
-
- getOptionParser() - Method in class net.sourceforge.seqware.pipeline.module.Module
-
getOptionParser.
- getOptionParser() - Method in class net.sourceforge.seqware.pipeline.modules.GenericCommandRunner
-
getOptionParser is an internal method to parse command line args.
- getOptionParser() - Method in class net.sourceforge.seqware.pipeline.modules.GenericMetadataSaver
-
Deprecated.
getOptionParser is an internal method to parse command line args.
- getOptionParser() - Method in class net.sourceforge.seqware.pipeline.modules.utilities.ProvisionDependenciesBundle
-
getOptionParser.
- getOptionParser() - Method in class net.sourceforge.seqware.pipeline.modules.utilities.ProvisionFiles
-
getOptionParser.
- getOptionParser() - Method in class net.sourceforge.seqware.pipeline.modules.utilities.S3CreateFileURLs
-
getOptionParser.
- getOptionParser() - Method in class net.sourceforge.seqware.pipeline.modules.utilities.S3DeleteFiles
-
getOptionParser.
- getOptionParser() - Method in class net.sourceforge.seqware.pipeline.modules.utilities.S3ListFiles
-
getOptionParser.
- getOptionParser() - Method in class net.sourceforge.seqware.pipeline.modules.utilities.S3UploadDirectory
-
- getOrganism() - Method in class net.sourceforge.seqware.common.model.Lane
-
Getter for the field organism.
- getOrganism() - Method in class net.sourceforge.seqware.common.model.Sample
-
Getter for the field
organism.
- getOrganism() - Method in class net.sourceforge.seqware.webservice.dto.LibraryDto
-
Getter for the field organism.
- getOrganismId() - Method in class io.seqware.webservice.generated.model.Lane
-
- getOrganismId() - Method in class io.seqware.webservice.generated.model.Organism
-
- getOrganismId() - Method in class io.seqware.webservice.generated.model.Sample
-
- getOrganismId() - Method in class net.sourceforge.seqware.common.model.Organism
-
Getter for the field organismId.
- getOrganismId() - Method in class net.sourceforge.seqware.common.model.Sample
-
Getter for the field
organismId.
- getOrganismId() - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.SampleInfo
-
- getOrganisms() - Method in interface net.sourceforge.seqware.common.metadata.Metadata
-
getOrganisms.
- getOrganisms() - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
-
- getOrganisms() - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection
-
- getOrganisms() - Method in class net.sourceforge.seqware.common.metadata.MetadataWS
-
- getOrganismService() - Method in class net.sourceforge.seqware.common.ContextImpl
-
- getOrganismService() - Method in class net.sourceforge.solexatools.webapp.controller.SampleController
-
Getter for the field organismService.
- getOrganismService() - Method in class net.sourceforge.solexatools.webapp.controller.SampleSetupController
-
Getter for the field organismService.
- getOrganismServiceBean() - Static method in class net.sourceforge.seqware.common.factory.BeanFactory
-
getOrganismServiceBean.
- getOriginalFileName() - Method in class net.sourceforge.seqware.common.util.filetools.ProvisionFilesUtil
-
Getter for the field originalFileName.
- getOs() - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object.WorkflowExecutable
-
- getOutput() - Method in class net.sourceforge.seqware.common.util.iotools.BufferedReaderThread
-
- getOutputDir() - Method in class net.sourceforge.seqware.pipeline.bundle.Bundle
-
Getter for the field outputDir.
- getOutputDir() - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object.OozieProvisionFileJob
-
- getOutputDir() - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object.ProvisionFilesJob
-
- getOutputFiles() - Method in class net.sourceforge.seqware.common.hibernate.reports.WorkflowRunReportRow
-
Getter for the field outputFiles.
- getOutputLineCapacity() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Command
-
- getOutputPath() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.SqwFile
-
- getOwner() - Method in class net.sourceforge.seqware.common.model.Experiment
-
Getter for the field owner.
- getOwner() - Method in class net.sourceforge.seqware.common.model.File
-
Getter for the field owner.
- getOwner() - Method in class net.sourceforge.seqware.common.model.Invoice
-
Getter for the field owner.
- getOwner() - Method in class net.sourceforge.seqware.common.model.IUS
-
Getter for the field owner.
- getOwner() - Method in class net.sourceforge.seqware.common.model.Lane
-
Getter for the field owner.
- getOwner() - Method in class net.sourceforge.seqware.common.model.Processing
-
Getter for the field owner.
- getOwner() - Method in class net.sourceforge.seqware.common.model.Sample
-
Getter for the field
owner.
- getOwner() - Method in class net.sourceforge.seqware.common.model.SequencerRun
-
Getter for the field owner.
- getOwner() - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
-
Getter for the field owner.
- getOwner() - Method in class net.sourceforge.seqware.common.model.Study
-
Getter for the field owner.
- getOwner() - Method in class net.sourceforge.seqware.common.model.Workflow
-
Getter for the field owner.
- getOwner() - Method in class net.sourceforge.seqware.common.model.WorkflowRun
-
Getter for the field owner.
- getOwner() - Method in class net.sourceforge.seqware.webservice.dto.LibraryDto
-
Getter for the field owner.
- getOwnerId() - Method in class io.seqware.webservice.generated.model.Experiment
-
- getOwnerId() - Method in class io.seqware.webservice.generated.model.File
-
- getOwnerId() - Method in class io.seqware.webservice.generated.model.Invoice
-
- getOwnerId() - Method in class io.seqware.webservice.generated.model.Ius
-
- getOwnerId() - Method in class io.seqware.webservice.generated.model.Lane
-
- getOwnerId() - Method in class io.seqware.webservice.generated.model.Processing
-
- getOwnerId() - Method in class io.seqware.webservice.generated.model.Sample
-
- getOwnerId() - Method in class io.seqware.webservice.generated.model.SequencerRun
-
- getOwnerId() - Method in class io.seqware.webservice.generated.model.Study
-
- getOwnerId() - Method in class io.seqware.webservice.generated.model.Workflow
-
- getOwnerId() - Method in class io.seqware.webservice.generated.model.WorkflowRun
-
- getOwnerUserName() - Method in class net.sourceforge.seqware.common.model.WorkflowRun
-
- getPage() - Method in class net.sourceforge.solexatools.webapp.metamodel.Flexigrid
-
Getter for the field page.
- getPageInfo(HttpServletRequest, String, List, List, String, String, MessageSourceAccessor) - Static method in class net.sourceforge.solexatools.util.PaginationUtil
-
getPageInfo.
- getPageInfoSD(HttpServletRequest, String, List, List, MessageSourceAccessor) - Static method in class net.sourceforge.solexatools.util.PaginationUtil
-
getPageInfoSD.
- getPageNumber(HttpServletRequest, Study, List<Study>) - Static method in class net.sourceforge.solexatools.util.PaginationUtil
-
getPageNumber.
- getPaidAmount() - Method in class io.seqware.webservice.generated.model.Invoice
-
- getPaidAmount() - Method in class net.sourceforge.seqware.common.model.Invoice
-
Getter for the field paidAmount.
- getPairedEnd() - Method in class io.seqware.webservice.generated.model.SequencerRun
-
- getPairedEnd() - Method in class net.sourceforge.seqware.common.model.SequencerRun
-
Getter for the field pairedEnd.
- getPairedEnd() - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
-
Getter for the field pairedEnd.
- getPairedEnd() - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.SampleInfo
-
- getPairedFilePath() - Method in class io.seqware.webservice.generated.model.SequencerRun
-
- getPairedFilePath() - Method in class net.sourceforge.seqware.common.model.SequencerRun
-
Getter for the field pairedFilePath.
- getPairedFilePath() - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
-
Getter for the field pairedFilePath.
- getPairedOrientation() - Method in class io.seqware.webservice.generated.model.ExperimentLibraryDesign
-
- getPairedOrientation() - Method in class net.sourceforge.seqware.common.model.ExperimentLibraryDesign
-
Getter for the field pairedOrientation.
- getParameters() - Method in class io.seqware.webservice.generated.model.Processing
-
- getParameters() - Method in class net.sourceforge.seqware.common.model.Processing
-
Getter for the field parameters.
- getParameters() - Method in class net.sourceforge.seqware.common.module.ReturnValue
-
Getter for the field parameters.
- getParameters() - Method in class net.sourceforge.seqware.pipeline.module.Module
-
Getter for the field parameters.
- getParams() - Method in class net.sourceforge.solexatools.util.SummaryLine
-
Getter for the field params.
- getParentAccessions() - Method in class net.sourceforge.seqware.pipeline.workflowV2.AbstractWorkflowDataModel
-
- getParentAccessions() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.AbstractJob
-
- getParentAccessions() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.SqwFile
-
- getParentId() - Method in class io.seqware.webservice.generated.model.ProcessingRelationship
-
- getParentId() - Method in class io.seqware.webservice.generated.model.SampleRelationship
-
- getParentId() - Method in class net.sourceforge.seqware.queryengine.webservice.model.SampleHierarchy
-
- getParentLane(Processing, Integer) - Static method in class net.sourceforge.solexatools.util.SequencerRunHtmlUtil
-
getParentLane.
- getParentProcessing(Processing, Integer) - Static method in class net.sourceforge.solexatools.util.SequencerRunHtmlUtil
-
getParentProcessing.
- getParentProcessingAccession() - Method in class io.seqware.webservice.generated.model.WorkflowRunParam
-
- getParentProcessingAccession() - Method in class net.sourceforge.seqware.common.model.WorkflowRunParam
-
Getter for the field parentProcessingAccession.
- getParentProcessings() - Method in class net.sourceforge.seqware.common.hibernate.reports.WorkflowRunReportRow
-
Getter for the field parentProcessings.
- getParents() - Method in class net.sourceforge.seqware.common.model.Processing
-
Getter for the field parents.
- getParents() - Method in class net.sourceforge.seqware.common.model.Sample
-
Getter for the field
parents.
- getParents() - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object.OozieJob
-
- getParents() - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object.PegasusJob
-
- getParents() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.AbstractJob
-
add all parent jobs
- getParents() - Method in interface net.sourceforge.seqware.pipeline.workflowV2.model.Job
-
- getParentSample() - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.SampleInfo
-
Get the value of parentSample
- getParentSamplesFrom(int) - Method in interface net.sourceforge.seqware.common.metadata.Metadata
-
Get the parent samples of a sample.
- getParentSamplesFrom(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
-
- getParentSamplesFrom(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection
-
- getParentSamplesFrom(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS
-
- getParentUrls() - Method in class net.sourceforge.seqware.webservice.dto.LibraryDto
-
Getter for the field parentUrls.
- getParentWorkflowAccessions() - Method in class net.sourceforge.seqware.pipeline.deciders.BasicDecider
-
- getPassword() - Method in class io.seqware.webservice.generated.model.Registration
-
- getPassword() - Method in class net.sourceforge.seqware.common.model.Registration
-
Getter for the field password.
- getPasswordHint() - Method in class io.seqware.webservice.generated.model.Registration
-
- getPasswordHint() - Method in class net.sourceforge.seqware.common.model.Registration
-
Getter for the field passwordHint.
- getPathToFirstFile() - Method in class net.sourceforge.seqware.common.model.UploadSequence
-
Getter for the field pathToFirstFile.
- getPathToSecondFile() - Method in class net.sourceforge.seqware.common.model.UploadSequence
-
Getter for the field pathToSecondFile.
- getPayee() - Method in class io.seqware.webservice.generated.model.Registration
-
- getPeakMemory() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Environment
-
- getPeakThreads() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Environment
-
- getPegasusConfigDir() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Environment
-
- getPending() - Method in class net.sourceforge.solexatools.webapp.metamodel.StudySampleReportLineItem
-
Getter for the field pending.
- getPermanentBundleLocation() - Method in class io.seqware.webservice.generated.model.Workflow
-
- getPermanentBundleLocation() - Method in class net.sourceforge.seqware.common.model.Workflow
-
Getter for the field permanentBundleLocation.
- getPermBundleLocation() - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowInfo
-
Getter for the field permBundleLocation.
- getPfn() - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object.WorkflowExecutable
-
- getPipelineJarPath() - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object.Adag
-
- getPlatform() - Method in class net.sourceforge.seqware.common.model.Experiment
-
Getter for the field platform.
- getPlatform() - Method in class net.sourceforge.seqware.common.model.SequencerRun
-
Getter for the field platform.
- getPlatform() - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
-
Getter for the field platform.
- getPlatformId() - Method in class io.seqware.webservice.generated.model.Experiment
-
- getPlatformId() - Method in class io.seqware.webservice.generated.model.Platform
-
- getPlatformId() - Method in class io.seqware.webservice.generated.model.SequencerRun
-
- getPlatformId() - Method in class net.sourceforge.seqware.common.model.Platform
-
Getter for the field platformId.
- getPlatformId() - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.RunInfo
-
- getPlatformInt() - Method in class net.sourceforge.seqware.common.model.Experiment
-
Getter for the field platformInt.
- getPlatformInt() - Method in class net.sourceforge.seqware.common.model.SequencerRun
-
Getter for the field platformInt.
- getPlatforms() - Method in interface net.sourceforge.seqware.common.metadata.Metadata
-
getPlatforms.
- getPlatforms() - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
-
- getPlatforms() - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection
-
- getPlatforms() - Method in class net.sourceforge.seqware.common.metadata.MetadataWS
-
- getPlatformService() - Method in class net.sourceforge.seqware.common.ContextImpl
-
Getter for the field platformService.
- getPlatformService() - Method in class net.sourceforge.solexatools.webapp.controller.ExperimentController
-
Getter for the field platformService.
- getPlatformService() - Method in class net.sourceforge.solexatools.webapp.controller.ExperimentSetupController
-
Getter for the field platformService.
- getPlatformService() - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunWizardController
-
Getter for the field platformService.
- getPlatformService() - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunWizardSetupController
-
Getter for the field platformService.
- getPlatformServiceBean() - Static method in class net.sourceforge.seqware.common.factory.BeanFactory
-
getPlatformServiceBean.
- getPOSTGRE_DB() - Static method in class net.sourceforge.seqware.metadb.util.TestDatabaseCreator
-
- getPOSTGRE_PASSWORD() - Method in class net.sourceforge.seqware.metadb.util.TestDatabaseCreator
-
- getPOSTGRE_USER() - Method in class net.sourceforge.seqware.metadb.util.TestDatabaseCreator
-
- getPricePerUnit() - Method in class io.seqware.webservice.generated.model.Expense
-
- getPricePerUnit() - Method in class net.sourceforge.seqware.common.model.Expense
-
Getter for the field
pricePerUnit.
- getPricePerUnitString() - Method in class net.sourceforge.seqware.common.model.Expense
-
Getter for the field
pricePerUnit.
- getPriority() - Method in class io.seqware.pipeline.plugins.sanity.checks.BundleDir_Check
-
- getPriority() - Method in class io.seqware.pipeline.plugins.sanity.checks.CLICheck
-
- getPriority() - Method in class io.seqware.pipeline.plugins.sanity.checks.DB_Check
-
- getPriority() - Method in class io.seqware.pipeline.plugins.sanity.checks.DB_WS_ConsistencyCheck
-
- getPriority() - Method in class io.seqware.pipeline.plugins.sanity.checks.HDFS_Check
-
- getPriority() - Method in class io.seqware.pipeline.plugins.sanity.checks.Oozie_Check
-
- getPriority() - Method in class io.seqware.pipeline.plugins.sanity.checks.Script_Check
-
- getPriority() - Method in class io.seqware.pipeline.plugins.sanity.checks.TutorialCheck
-
- getPriority() - Method in class io.seqware.pipeline.plugins.sanity.checks.WS_Check
-
- getPriority() - Method in interface io.seqware.pipeline.plugins.sanity.SanityCheckPluginInterface
-
Indicate the priority of the check, higher is later
- getPrivate() - Method in class net.sourceforge.seqware.common.model.Workflow
-
getPrivate.
- getProcess() - Method in class io.seqware.webservice.generated.model.SequencerRun
-
- getProcess() - Method in class net.sourceforge.seqware.common.model.SequencerRun
-
Getter for the field process.
- getProcessedCnt(SequencerRun) - Method in class net.sourceforge.seqware.common.dao.hibernate.SequencerRunDAOHibernate
-
getProcessedCnt.
- getProcessedCnt(SequencerRun) - Method in interface net.sourceforge.seqware.common.dao.SequencerRunDAO
-
Deprecated.
- getProcessedCnt() - Method in class net.sourceforge.seqware.common.model.Lane
-
getProcessedCnt.
- getProcessedCnt() - Method in class net.sourceforge.seqware.common.model.SequencerRun
-
getProcessedCnt.
- getProcessedCount() - Method in class net.sourceforge.seqware.common.model.SequencerRun
-
Getter for the field processedCount.
- getProcessExitStatus() - Method in class io.seqware.webservice.generated.model.Processing
-
- getProcessExitStatus() - Method in class net.sourceforge.seqware.common.model.Processing
-
Getter for the field processExitStatus.
- getProcessExitStatus() - Method in class net.sourceforge.seqware.common.module.ReturnValue
-
Getter for the field processExitStatus.
- getProcessing(int) - Method in interface net.sourceforge.seqware.common.metadata.Metadata
-
getProcessing.
- getProcessing(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
-
- getProcessing(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection
-
- getProcessing(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS
-
- getProcessing() - Method in class net.sourceforge.seqware.common.model.FileReportRow
-
Getter for the field processing.
- getProcessing() - Method in class net.sourceforge.seqware.common.model.ProcessingAttribute
-
Getter for the field processing.
- getProcessing() - Method in class net.sourceforge.seqware.common.model.ProcessingExperiments
-
Getter for the field processing.
- getProcessing() - Method in class net.sourceforge.seqware.common.model.ProcessingIus
-
Getter for the field processing.
- getProcessing() - Method in class net.sourceforge.seqware.common.model.ProcessingLanes
-
Getter for the field processing.
- getProcessing() - Method in class net.sourceforge.seqware.common.model.ProcessingSamples
-
Getter for the field processing.
- getProcessing() - Method in class net.sourceforge.seqware.common.model.ProcessingSequencerRuns
-
Getter for the field processing.
- getProcessing() - Method in class net.sourceforge.seqware.common.model.ProcessingStudies
-
Getter for the field processing.
- getProcessing() - Method in class net.sourceforge.seqware.common.model.ShareProcessing
-
Getter for the field processing.
- getProcessingAccession() - Method in class net.sourceforge.seqware.pipeline.module.Module
-
Getter for the field processingAccession.
- getProcessingAttributeCollection() - Method in class io.seqware.webservice.generated.model.Processing
-
- getProcessingAttributeId() - Method in class io.seqware.webservice.generated.model.ProcessingAttribute
-
- getProcessingAttributeId() - Method in class net.sourceforge.seqware.common.model.ProcessingAttribute
-
Getter for the field processingAttributeId.
- getProcessingAttributes() - Method in class net.sourceforge.seqware.common.model.Processing
-
Getter for the field processingAttributes.
- getProcessingByChildId() - Method in class net.sourceforge.seqware.common.model.ProcessingRelationship
-
Getter for the field processingByChildId.
- getProcessingByParentId() - Method in class net.sourceforge.seqware.common.model.ProcessingRelationship
-
Getter for the field processingByParentId.
- getProcessingCnt(SequencerRun) - Method in class net.sourceforge.seqware.common.dao.hibernate.SequencerRunDAOHibernate
-
getProcessingCnt.
- getProcessingCnt(SequencerRun) - Method in interface net.sourceforge.seqware.common.dao.SequencerRunDAO
-
Deprecated.
- getProcessingCnt() - Method in class net.sourceforge.seqware.common.model.Lane
-
getProcessingCnt.
- getProcessingCnt() - Method in class net.sourceforge.seqware.common.model.SequencerRun
-
getProcessingCnt.
- getProcessingCnt() - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
-
getProcessingCnt.
- getProcessingCollection() - Method in class io.seqware.webservice.generated.model.Registration
-
- getProcessingCollection() - Method in class io.seqware.webservice.generated.model.WorkflowRun
-
- getProcessingCollection1() - Method in class io.seqware.webservice.generated.model.WorkflowRun
-
- getProcessingCount() - Method in class net.sourceforge.seqware.common.model.SequencerRun
-
Getter for the field processingCount.
- getProcessingExperimentsCollection() - Method in class io.seqware.webservice.generated.model.Experiment
-
- getProcessingExperimentsCollection() - Method in class io.seqware.webservice.generated.model.Processing
-
- getProcessingExperimentServiceBean() - Static method in class net.sourceforge.seqware.common.factory.BeanFactory
-
getProcessingExperimentServiceBean.
- getProcessingExperimentsId() - Method in class io.seqware.webservice.generated.model.ProcessingExperiments
-
- getProcessingExperimentsId() - Method in class net.sourceforge.seqware.common.model.ProcessingExperiments
-
Getter for the field processingExperimentsId.
- getProcessingExperimentsService() - Method in class net.sourceforge.seqware.common.ContextImpl
-
Getter for the field processingExperimentsService.
- getProcessingFilesCollection() - Method in class io.seqware.webservice.generated.model.File
-
- getProcessingFilesCollection() - Method in class io.seqware.webservice.generated.model.Processing
-
- getProcessingFilesId() - Method in class io.seqware.webservice.generated.model.ProcessingFiles
-
- getProcessingHtml(Processing, Registration, String, String, String) - Static method in class net.sourceforge.solexatools.util.NodeHtmlUtil
-
getProcessingHtml.
- getProcessingId() - Method in class io.seqware.webservice.generated.model.FileReport
-
- getProcessingId() - Method in class io.seqware.webservice.generated.model.Processing
-
- getProcessingId() - Method in class io.seqware.webservice.generated.model.ProcessingAttribute
-
- getProcessingId() - Method in class io.seqware.webservice.generated.model.ProcessingExperiments
-
- getProcessingId() - Method in class io.seqware.webservice.generated.model.ProcessingFiles
-
- getProcessingId() - Method in class io.seqware.webservice.generated.model.ProcessingIus
-
- getProcessingId() - Method in class io.seqware.webservice.generated.model.ProcessingLanes
-
- getProcessingId() - Method in class io.seqware.webservice.generated.model.ProcessingSamples
-
- getProcessingId() - Method in class io.seqware.webservice.generated.model.ProcessingSequencerRuns
-
- getProcessingId() - Method in class io.seqware.webservice.generated.model.ProcessingStudies
-
- getProcessingId() - Method in class io.seqware.webservice.generated.model.ShareProcessing
-
- getProcessingId() - Method in class net.sourceforge.seqware.common.model.Processing
-
Getter for the field processingId.
- getProcessingIusCollection() - Method in class io.seqware.webservice.generated.model.Ius
-
- getProcessingIusCollection() - Method in class io.seqware.webservice.generated.model.Processing
-
- getProcessingIusId() - Method in class io.seqware.webservice.generated.model.ProcessingIus
-
- getProcessingIusId() - Method in class net.sourceforge.seqware.common.model.ProcessingIus
-
Getter for the field processingIusId.
- getProcessingIusService() - Method in class net.sourceforge.seqware.common.ContextImpl
-
Getter for the field processingIusService.
- getProcessingIUSServiceBean() - Static method in class net.sourceforge.seqware.common.factory.BeanFactory
-
getProcessingIUSServiceBean.
- getProcessingLanesCollection() - Method in class io.seqware.webservice.generated.model.Lane
-
- getProcessingLanesCollection() - Method in class io.seqware.webservice.generated.model.Processing
-
- getProcessingLaneService() - Method in class net.sourceforge.seqware.common.ContextImpl
-
Getter for the field processingLaneService.
- getProcessingLaneServiceBean() - Static method in class net.sourceforge.seqware.common.factory.BeanFactory
-
getProcessingLaneServiceBean.
- getProcessingLanesId() - Method in class io.seqware.webservice.generated.model.ProcessingLanes
-
- getProcessingLanesId() - Method in class net.sourceforge.seqware.common.model.ProcessingLanes
-
Getter for the field processingLanesId.
- getProcessingRelations(String) - Method in interface net.sourceforge.seqware.common.metadata.Metadata
-
getProcessingRelations.
- getProcessingRelations(String) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
-
- getProcessingRelations(String) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection
-
- getProcessingRelations(String) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS
-
- getProcessingRelationshipCollection() - Method in class io.seqware.webservice.generated.model.Processing
-
- getProcessingRelationshipCollection1() - Method in class io.seqware.webservice.generated.model.Processing
-
- getProcessingRelationshipId() - Method in class io.seqware.webservice.generated.model.ProcessingRelationship
-
- getProcessingRelationshipId() - Method in class net.sourceforge.seqware.common.model.ProcessingRelationship
-
Getter for the field processingRelationshipId.
- getProcessingRelationshipService() - Method in class net.sourceforge.seqware.common.ContextImpl
-
Getter for the field processingRelationshipService.
- getProcessingRelationshipServiceBean() - Static method in class net.sourceforge.seqware.common.factory.BeanFactory
-
getProcessingRelationshipServiceBean.
- getProcessings() - Method in class net.sourceforge.seqware.common.model.Experiment
-
Getter for the field processings.
- getProcessings() - Method in class net.sourceforge.seqware.common.model.File
-
Getter for the field processings.
- getProcessings() - Method in class net.sourceforge.seqware.common.model.IUS
-
Getter for the field processings.
- getProcessings() - Method in class net.sourceforge.seqware.common.model.Lane
-
Getter for the field processings.
- getProcessings() - Method in class net.sourceforge.seqware.common.model.Sample
-
Getter for the field
processings.
- getProcessings() - Method in class net.sourceforge.seqware.common.model.SequencerRun
-
Getter for the field processings.
- getProcessings() - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
-
Getter for the field processings.
- getProcessings() - Method in class net.sourceforge.seqware.common.model.Study
-
Getter for the field processings.
- getProcessings() - Method in class net.sourceforge.seqware.common.model.WorkflowRun
-
Getter for the field processings.
- getProcessingSamplesCollection() - Method in class io.seqware.webservice.generated.model.Processing
-
- getProcessingSamplesCollection() - Method in class io.seqware.webservice.generated.model.Sample
-
- getProcessingSampleServiceBean() - Static method in class net.sourceforge.seqware.common.factory.BeanFactory
-
getProcessingSampleServiceBean.
- getProcessingSamplesId() - Method in class io.seqware.webservice.generated.model.ProcessingSamples
-
- getProcessingSamplesId() - Method in class net.sourceforge.seqware.common.model.ProcessingSamples
-
Getter for the field processingSamplesId.
- getProcessingSamplesService() - Method in class net.sourceforge.seqware.common.ContextImpl
-
Getter for the field processingSamplesService.
- getProcessingsByWorkflow(WorkflowRun) - Method in class net.sourceforge.solexatools.webapp.metamodel.SampleDetailsWorkflowLineItems
-
getProcessingsByWorkflow.
- getProcessingSequencerRunsCollection() - Method in class io.seqware.webservice.generated.model.Processing
-
- getProcessingSequencerRunsCollection() - Method in class io.seqware.webservice.generated.model.SequencerRun
-
- getProcessingSequencerRunService() - Method in class net.sourceforge.seqware.common.ContextImpl
-
Getter for the field processingSequencerRunService.
- getProcessingSequencerRunsId() - Method in class io.seqware.webservice.generated.model.ProcessingSequencerRuns
-
- getProcessingSequencerRunsId() - Method in class net.sourceforge.seqware.common.model.ProcessingSequencerRuns
-
Getter for the field processingSequencerRunsId.
- getProcessingSequencerRunsServiceBean() - Static method in class net.sourceforge.seqware.common.factory.BeanFactory
-
getProcessingSequencerRunsServiceBean.
- getProcessingService() - Method in class net.sourceforge.seqware.common.ContextImpl
-
Getter for the field processingService.
- getProcessingService() - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysBulkDownloadListDetailsController
-
Getter for the field processingService.
- getProcessingService() - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysListDetailsController
-
Getter for the field processingService.
- getProcessingService() - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysRunningListDetailsController
-
Getter for the field processingService.
- getProcessingService() - Method in class net.sourceforge.solexatools.webapp.controller.BulkDownloadListDetailsController
-
Getter for the field processingService.
- getProcessingService() - Method in class net.sourceforge.solexatools.webapp.controller.DownloadFileListController
-
Getter for the field processingService.
- getProcessingService() - Method in class net.sourceforge.solexatools.webapp.controller.LaunchWorkflowListDetailsController
-
Getter for the field processingService.
- getProcessingService() - Method in class net.sourceforge.solexatools.webapp.controller.ProcessingController
-
Getter for the field processingService.
- getProcessingService() - Method in class net.sourceforge.solexatools.webapp.controller.ProcessingSetupController
-
Getter for the field processingService.
- getProcessingService() - Method in class net.sourceforge.solexatools.webapp.controller.SaveOpenNodeController
-
Getter for the field processingService.
- getProcessingService() - Method in class net.sourceforge.solexatools.webapp.controller.SelectInputListController
-
Getter for the field processingService.
- getProcessingService() - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunListDetailsController
-
Getter for the field processingService.
- getProcessingService() - Method in class net.sourceforge.solexatools.webapp.controller.StudyListDetailsController
-
Getter for the field processingService.
- getProcessingService() - Method in class net.sourceforge.solexatools.webapp.controller.StudyListDetailsFlatController
-
Getter for the field processingService.
- getProcessingService() - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileController
-
Getter for the field processingService.
- getProcessingService() - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileSetupController
-
Getter for the field processingService.
- getProcessingService() - Method in class net.sourceforge.solexatools.webapp.controller.UploadSequenceController
-
Getter for the field processingService.
- getProcessingServiceBean() - Static method in class net.sourceforge.seqware.common.factory.BeanFactory
-
getProcessingServiceBean.
- getProcessingStudiesCollection() - Method in class io.seqware.webservice.generated.model.Processing
-
- getProcessingStudiesCollection() - Method in class io.seqware.webservice.generated.model.Study
-
- getProcessingStudiesId() - Method in class io.seqware.webservice.generated.model.ProcessingStudies
-
- getProcessingStudiesId() - Method in class net.sourceforge.seqware.common.model.ProcessingStudies
-
Getter for the field processingStudiesId.
- getProcessingStudiesService() - Method in class net.sourceforge.seqware.common.ContextImpl
-
Getter for the field processingStudiesService.
- getProcessingStudiesServiceBean() - Static method in class net.sourceforge.seqware.common.factory.BeanFactory
-
getProcessingStudiesServiceBean.
- getProcStatuses(SequencerRun) - Method in class net.sourceforge.seqware.common.dao.hibernate.SequencerRunDAOHibernate
-
getProcStatuses.
- getProcStatuses(SequencerRun) - Method in interface net.sourceforge.seqware.common.dao.SequencerRunDAO
-
Deprecated.
- getProjectCode() - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.SampleInfo
-
- getProjectId() - Method in class io.seqware.webservice.generated.model.Study
-
- getProjectId() - Method in class net.sourceforge.seqware.common.model.Study
-
Getter for the field projectId.
- getProperty(String) - Static method in class net.sourceforge.seqware.common.util.configtools.ConfigTools
-
getProperty.
- getProperty(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.AbstractWorkflowDataModel
-
get the user defined INI files properties
- getProperty(String) - Static method in class net.sourceforge.seqware.queryengine.webservice.util.EnvUtil
-
getProperty.
- getProvisionedPath() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.SqwFile
-
- getPublic() - Method in class net.sourceforge.seqware.common.model.Workflow
-
getPublic.
- getQsubOptions() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.AbstractJob
-
- getQualityMultiplier() - Method in class io.seqware.webservice.generated.model.Experiment
-
- getQualityMultiplier() - Method in class net.sourceforge.seqware.common.model.Experiment
-
Getter for the field qualityMultiplier.
- getQualityNumberOfLevels() - Method in class io.seqware.webservice.generated.model.Experiment
-
- getQualityNumberOfLevels() - Method in class net.sourceforge.seqware.common.model.Experiment
-
Getter for the field qualityNumberOfLevels.
- getQualityScorer() - Method in class io.seqware.webservice.generated.model.Experiment
-
- getQualityScorer() - Method in class io.seqware.webservice.generated.model.SequencerRun
-
- getQualityScorer() - Method in class net.sourceforge.seqware.common.model.Experiment
-
Getter for the field qualityScorer.
- getQualityType() - Method in class io.seqware.webservice.generated.model.Experiment
-
- getQualityType() - Method in class net.sourceforge.seqware.common.model.Experiment
-
Getter for the field qualityType.
- getQueryValue(String) - Method in class net.sourceforge.seqware.webservice.resources.BasicRestlet
-
- getQueue() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.AbstractJob
-
- getQueue() - Method in interface net.sourceforge.seqware.pipeline.workflowV2.model.Job
-
- getRandom() - Method in class net.sourceforge.seqware.pipeline.workflowV2.AbstractWorkflowDataModel
-
- getReadClass() - Method in class io.seqware.webservice.generated.model.ExperimentSpotDesignReadSpec
-
- getReadClass() - Method in class net.sourceforge.seqware.common.model.ExperimentSpotDesignReadSpec
-
Getter for the field readClass.
- getReader() - Method in class net.sourceforge.seqware.common.util.iotools.BufferedReaderThread
-
Getter for the field reader.
- getReadIndex() - Method in class io.seqware.webservice.generated.model.ExperimentSpotDesignReadSpec
-
- getReadIndex() - Method in class net.sourceforge.seqware.common.model.ExperimentSpotDesignReadSpec
-
Getter for the field readIndex.
- getReadLabel() - Method in class io.seqware.webservice.generated.model.ExperimentSpotDesignReadSpec
-
- getReadLabel() - Method in class net.sourceforge.seqware.common.model.ExperimentSpotDesignReadSpec
-
Getter for the field readLabel.
- getReadSpec() - Method in class io.seqware.webservice.generated.model.ExperimentSpotDesign
-
- getReadSpec() - Method in class net.sourceforge.seqware.common.model.ExperimentSpotDesign
-
Getter for the field readSpec.
- getReadSpecs() - Method in class net.sourceforge.seqware.common.model.ExperimentSpotDesign
-
Getter for the field readSpecs.
- getReadsPerSpot() - Method in class io.seqware.webservice.generated.model.ExperimentSpotDesign
-
- getReadsPerSpot() - Method in class net.sourceforge.seqware.common.model.ExperimentSpotDesign
-
Getter for the field readsPerSpot.
- getReadType() - Method in class io.seqware.webservice.generated.model.ExperimentSpotDesignReadSpec
-
- getReadType() - Method in class net.sourceforge.seqware.common.model.ExperimentSpotDesignReadSpec
-
Getter for the field readType.
- getReadyToProcess() - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
-
Getter for the field readyToProcess.
- getRefLane() - Method in class io.seqware.webservice.generated.model.SequencerRun
-
- getRefLane() - Method in class net.sourceforge.seqware.common.model.SequencerRun
-
Getter for the field refLane.
- getRefLane() - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
-
Getter for the field refLane.
- getRegions() - Method in class io.seqware.webservice.generated.model.Lane
-
- getRegions() - Method in class io.seqware.webservice.generated.model.Sample
-
- getRegions() - Method in class net.sourceforge.seqware.common.model.Lane
-
Getter for the field regions.
- getRegions() - Method in class net.sourceforge.seqware.common.model.Sample
-
Getter for the field
regions.
- getRegistration() - Method in class net.sourceforge.seqware.common.model.ShareExperiment
-
Getter for the field registration.
- getRegistration() - Method in class net.sourceforge.seqware.common.model.ShareFile
-
Getter for the field registration.
- getRegistration() - Method in class net.sourceforge.seqware.common.model.ShareLane
-
Getter for the field registration.
- getRegistration() - Method in class net.sourceforge.seqware.common.model.ShareProcessing
-
Getter for the field registration.
- getRegistration() - Method in class net.sourceforge.seqware.common.model.ShareSample
-
Getter for the field registration.
- getRegistration() - Method in class net.sourceforge.seqware.common.model.ShareStudy
-
Getter for the field registration.
- getRegistration() - Method in class net.sourceforge.seqware.common.model.ShareWorkflowRun
-
Getter for the field registration.
- getRegistration(HttpServletRequest) - Static method in class net.sourceforge.solexatools.Security
-
getRegistration.
- getRegistrationId() - Method in class io.seqware.webservice.generated.model.Registration
-
- getRegistrationId() - Method in class io.seqware.webservice.generated.model.ShareExperiment
-
- getRegistrationId() - Method in class io.seqware.webservice.generated.model.ShareFile
-
- getRegistrationId() - Method in class io.seqware.webservice.generated.model.ShareLane
-
- getRegistrationId() - Method in class io.seqware.webservice.generated.model.ShareProcessing
-
- getRegistrationId() - Method in class io.seqware.webservice.generated.model.ShareSample
-
- getRegistrationId() - Method in class io.seqware.webservice.generated.model.ShareStudy
-
- getRegistrationId() - Method in class io.seqware.webservice.generated.model.ShareWorkflowRun
-
- getRegistrationId() - Method in class net.sourceforge.seqware.common.model.Registration
-
Getter for the field registrationId.
- getRegistrationService() - Method in class net.sourceforge.seqware.common.ContextImpl
-
Getter for the field registrationService.
- getRegistrationService() - Method in class net.sourceforge.solexatools.webapp.controller.InviteNewUserController
-
Getter for the field registrationService.
- getRegistrationService() - Method in class net.sourceforge.solexatools.webapp.controller.InviteNewUserValidatorController
-
Getter for the field registrationService.
- getRegistrationService() - Method in class net.sourceforge.solexatools.webapp.controller.LoginController
-
Getter for the field registrationService.
- getRegistrationService() - Method in class net.sourceforge.solexatools.webapp.controller.RegistrationController
-
Getter for the field registrationService.
- getRegistrationService() - Method in class net.sourceforge.solexatools.webapp.controller.RegistrationSetupController
-
Getter for the field registrationService.
- getRegistrationService() - Method in class net.sourceforge.solexatools.webapp.controller.ShareValidatorController
-
Getter for the field registrationService.
- getRegistrationService() - Method in class net.sourceforge.solexatools.webapp.controller.SignUpController
-
Getter for the field registrationService.
- getRegistrationServiceBean() - Static method in class net.sourceforge.seqware.common.factory.BeanFactory
-
getRegistrationServiceBean.
- getRelationship() - Method in class io.seqware.webservice.generated.model.ProcessingRelationship
-
- getRelationship() - Method in class io.seqware.webservice.generated.model.SampleRelationship
-
- getRelationship() - Method in class net.sourceforge.seqware.common.model.ProcessingRelationship
-
Getter for the field relationship.
- getReportForSequencerRun(SequencerRun, String, String, int, int) - Method in interface net.sourceforge.seqware.common.business.FileReportService
-
getReportForSequencerRun.
- getReportForSequencerRun(SequencerRun, String, String) - Method in interface net.sourceforge.seqware.common.business.FileReportService
-
getReportForSequencerRun.
- getReportForSequencerRun(SequencerRun) - Method in interface net.sourceforge.seqware.common.business.FileReportService
-
getReportForSequencerRun.
- getReportForSequencerRun(SequencerRun, String, String, int, int) - Method in class net.sourceforge.seqware.common.business.impl.FileReportServiceImpl
-
getReportForSequencerRun.
- getReportForSequencerRun(SequencerRun, String, String) - Method in class net.sourceforge.seqware.common.business.impl.FileReportServiceImpl
-
getReportForSequencerRun.
- getReportForSequencerRun(SequencerRun) - Method in class net.sourceforge.seqware.common.business.impl.FileReportServiceImpl
-
getReportForSequencerRun.
- getReportForSequencerRun(SequencerRun, String, String, int, int) - Method in interface net.sourceforge.seqware.common.dao.FileReportDAO
-
getReportForSequencerRun.
- getReportForSequencerRun(SequencerRun) - Method in interface net.sourceforge.seqware.common.dao.FileReportDAO
-
getReportForSequencerRun.
- getReportForSequencerRun(SequencerRun, String, String, int, int) - Method in class net.sourceforge.seqware.common.dao.hibernate.FileReportDAOHibernate
-
getReportForSequencerRun.
- getReportForSequencerRun(SequencerRun) - Method in class net.sourceforge.seqware.common.dao.hibernate.FileReportDAOHibernate
-
getReportForSequencerRun.
- getReportForSequencerRuns(String, String, int, int) - Method in interface net.sourceforge.seqware.common.dao.FileReportDAO
-
getReportForSequencerRuns.
- getReportForSequencerRuns(String, String, int, int) - Method in class net.sourceforge.seqware.common.dao.hibernate.FileReportDAOHibernate
-
getReportForSequencerRuns.
- getReportForStudy(Study) - Method in interface net.sourceforge.seqware.common.business.FileReportService
-
getReportForStudy.
- getReportForStudy(Study, String, String, int, int) - Method in interface net.sourceforge.seqware.common.business.FileReportService
-
getReportForStudy.
- getReportForStudy(Study) - Method in class net.sourceforge.seqware.common.business.impl.FileReportServiceImpl
-
getReportForStudy.
- getReportForStudy(Study, String, String, int, int) - Method in class net.sourceforge.seqware.common.business.impl.FileReportServiceImpl
-
getReportForStudy.
- getReportForStudy(Study) - Method in interface net.sourceforge.seqware.common.dao.FileReportDAO
-
getReportForStudy.
- getReportForStudy(Study, String, String, int, int) - Method in interface net.sourceforge.seqware.common.dao.FileReportDAO
-
getReportForStudy.
- getReportForStudy(Study) - Method in class net.sourceforge.seqware.common.dao.hibernate.FileReportDAOHibernate
-
getReportForStudy.
- getReportForStudy(Study, String, String, int, int) - Method in class net.sourceforge.seqware.common.dao.hibernate.FileReportDAOHibernate
-
getReportForStudy.
- getRepresentation(Document) - Static method in class net.sourceforge.seqware.common.util.xmltools.XmlTools
-
getRepresentation.
- getRequestedTypeList(HttpServletRequest) - Static method in class net.sourceforge.solexatools.util.ControllerUtil
-
getRequestedTypeList.
- getRequestedTypeList(HttpServletRequest) - Method in class net.sourceforge.solexatools.webapp.controller.StudyListDetailsController
-
getRequestedTypeList.
- getRequirements() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.AbstractJob
-
get job requirements
- getResourceInfo(ApplicationInfo) - Method in class net.sourceforge.seqware.webservice.resources.queries.GenericDBResource
- getReturnValue() - Method in exception net.sourceforge.seqware.common.err.OldSeqwareException
-
Getter for the field returnValue.
- getReturnValue() - Method in class net.sourceforge.seqware.common.module.ReturnValue
-
Getter for the field returnValue.
- getReturnValues() - Method in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles
-
Getter for the field returnValues.
- getRootProcessing(Integer) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowRunServiceImpl
-
getRootProcessing.
- getRootProcessing(Integer) - Method in interface net.sourceforge.seqware.common.business.WorkflowRunService
-
getRootProcessing.
- getRootProcessing(WorkflowRun) - Static method in class net.sourceforge.solexatools.util.FindChildUtil
-
getRootProcessing.
- getRootProcessingName() - Method in class net.sourceforge.seqware.common.business.impl.ValidationReportServiceImpl.ReportEntry
-
- getRootProcessingSwa() - Method in class net.sourceforge.seqware.common.business.impl.ValidationReportServiceImpl.ReportEntry
-
- getRootSample(Sample) - Method in class net.sourceforge.seqware.common.business.impl.SampleServiceImpl
-
getRootSample.
- getRootSample(Sample) - Method in interface net.sourceforge.seqware.common.business.SampleService
-
getRootSample.
- getRootSample(Sample) - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleDAOHibernate
-
getRootSample.
- getRootSample(Sample) - Method in interface net.sourceforge.seqware.common.dao.SampleDAO
-
getRootSample.
- getRootSample() - Method in class net.sourceforge.solexatools.webapp.metamodel.StudySampleReportFileLineItem
-
Getter for the field rootSample.
- getRootSamples(Study) - Method in class net.sourceforge.seqware.common.business.impl.SampleServiceImpl
-
getRootSamples.
- getRootSamples(Study) - Method in interface net.sourceforge.seqware.common.business.SampleService
-
getRootSamples.
- getRootSamples(Study) - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleDAOHibernate
-
getRootSamples.
- getRootSamples(Study) - Method in interface net.sourceforge.seqware.common.dao.SampleDAO
-
getRootSamples.
- getRowId() - Method in class io.seqware.webservice.generated.model.FileReport
-
- getRowId() - Method in class io.seqware.webservice.generated.model.SampleReport
-
- getRowId() - Method in class net.sourceforge.seqware.common.model.FileReportRow
-
Getter for the field rowId.
- getRowId() - Method in class net.sourceforge.seqware.common.model.SampleReportRow
-
Getter for the field rowId.
- getRows() - Method in class net.sourceforge.solexatools.webapp.metamodel.Flexigrid
-
Getter for the field rows.
- getRowsForSequencerRun(SequencerRun) - Method in class net.sourceforge.seqware.common.business.impl.SampleReportServiceImpl
-
getRowsForSequencerRun.
- getRowsForSequencerRun(SequencerRun) - Method in interface net.sourceforge.seqware.common.business.SampleReportService
-
getRowsForSequencerRun.
- getRowsForSequencerRun(SequencerRun) - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleReportDAOHibernate
-
getRowsForSequencerRun.
- getRowsForSequencerRun(SequencerRun) - Method in interface net.sourceforge.seqware.common.dao.SampleReportDAO
-
getRowsForSequencerRun.
- getRowsWithSequencerRuns() - Method in class net.sourceforge.seqware.common.business.impl.SampleReportServiceImpl
-
getRowsWithSequencerRuns.
- getRowsWithSequencerRuns() - Method in interface net.sourceforge.seqware.common.business.SampleReportService
-
getRowsWithSequencerRuns.
- getRowsWithSequencerRuns() - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleReportDAOHibernate
-
getRowsWithSequencerRuns.
- getRowsWithSequencerRuns() - Method in interface net.sourceforge.seqware.common.dao.SampleReportDAO
-
getRowsWithSequencerRuns.
- getRunAttributes() - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.RunInfo
-
Get the value of runAttributes
- getRunCenter() - Method in class io.seqware.webservice.generated.model.SequencerRun
-
- getRunCenter() - Method in class net.sourceforge.seqware.common.model.SequencerRun
-
Getter for the field runCenter.
- getRunCenter() - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
-
Getter for the field runCenter.
- getRunDescription() - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.RunInfo
-
Get the value of runDescription
- getRunFilePath() - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.RunInfo
-
Get the value of runFilePath
- getRunInfo() - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.CreateFromScratch
-
- getRunName() - Method in class net.sourceforge.seqware.common.hibernate.SequencerRunReport.Row
-
- getRunName() - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.RunInfo
-
Get the value of runName
- getRunningCount(Study) - Method in class net.sourceforge.seqware.common.business.impl.StudyServiceImpl
-
getRunningCount.
- getRunningCount(Study) - Method in interface net.sourceforge.seqware.common.business.StudyService
-
getRunningCount.
- getRunsFromWorkflow(Integer) - Method in class net.sourceforge.seqware.common.hibernate.WorkflowRunReport
-
Using a workflow SWID, find all of the workflow runs, and report on each
of the workflow runs the files, samples and processing events associated
with each.
- getRunSkip() - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.RunInfo
-
Get the value of runSkip
- getRunStartTimestamp() - Method in class net.sourceforge.seqware.common.model.Processing
-
Getter for the field runStartTimestamp.
- getRunStartTstmp() - Method in class io.seqware.webservice.generated.model.Processing
-
- getRunStartTstmp() - Method in class net.sourceforge.seqware.common.module.ReturnValue
-
Getter for the field runStartTstmp.
- getRunStopTimestamp() - Method in class net.sourceforge.seqware.common.model.Processing
-
Getter for the field runStopTimestamp.
- getRunStopTstmp() - Method in class io.seqware.webservice.generated.model.Processing
-
- getRunStopTstmp() - Method in class net.sourceforge.seqware.common.module.ReturnValue
-
Getter for the field runStopTstmp.
- getRunSwa() - Method in class net.sourceforge.seqware.common.hibernate.SequencerRunReport.Row
-
- getS3InputStream(String, int, long, String, String) - Method in class net.sourceforge.seqware.common.util.filetools.ProvisionFilesUtil
-
getS3InputStream.
- getS3InputStream(String, int, long) - Method in class net.sourceforge.seqware.common.util.filetools.ProvisionFilesUtil
-
getS3InputStream.
- getS3Url(String) - Method in class net.sourceforge.seqware.common.util.filetools.ProvisionFilesUtil
-
getS3Url.
- getS3Url(String, String, String) - Method in class net.sourceforge.seqware.common.util.filetools.ProvisionFilesUtil
-
getS3Url.
- getSample() - Method in class net.sourceforge.seqware.common.model.FileReportRow
-
Getter for the field sample.
- getSample() - Method in class net.sourceforge.seqware.common.model.IUS
-
Getter for the field sample.
- getSample() - Method in class net.sourceforge.seqware.common.model.Lane
-
Getter for the field sample.
- getSample() - Method in class net.sourceforge.seqware.common.model.ProcessingSamples
-
Getter for the field sample.
- getSample() - Method in class net.sourceforge.seqware.common.model.SampleAttribute
-
Getter for the field sample.
- getSample() - Method in class net.sourceforge.seqware.common.model.SampleLink
-
Getter for the field sample.
- getSample() - Method in class net.sourceforge.seqware.common.model.SampleSearch
-
Getter for the field sample.
- getSample() - Method in class net.sourceforge.seqware.common.model.ShareSample
-
Getter for the field sample.
- getSample() - Method in class net.sourceforge.seqware.common.model.UploadSequence
-
Getter for the field sample.
- getSample() - Method in class net.sourceforge.seqware.common.model.WorkflowParam
-
Getter for the field sample.
- getSample() - Method in class net.sourceforge.seqware.pipeline.plugins.filelinker.FileLinkerLine
-
- getSample() - Method in class net.sourceforge.solexatools.webapp.metamodel.StudySampleReportLineItem
-
Getter for the field sample.
- getSample_url() - Method in class net.sourceforge.seqware.webservice.dto.IusDto
-
Getter for the field sample_url.
- getSampleAttributeCollection() - Method in class io.seqware.webservice.generated.model.Sample
-
- getSampleAttributeId() - Method in class io.seqware.webservice.generated.model.SampleAttribute
-
- getSampleAttributeId() - Method in class net.sourceforge.seqware.common.model.SampleAttribute
-
Getter for the field sampleAttributeId.
- getSampleAttributes() - Method in class net.sourceforge.seqware.common.model.Sample
-
Getter for the field
sampleAttributes.
- getSampleAttributes() - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.SampleInfo
-
Get the value of sampleAttributes
- getSampleByName(String) - Method in interface net.sourceforge.seqware.common.metadata.Metadata
-
- getSampleByName(String) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
-
- getSampleByName(String) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection
-
- getSampleByName(String) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS
-
- getSampleCode() - Method in class net.sourceforge.seqware.common.model.Lane
-
Getter for the field sampleCode.
- getSampleCollection() - Method in class io.seqware.webservice.generated.model.Experiment
-
- getSampleCollection() - Method in class io.seqware.webservice.generated.model.Organism
-
- getSampleCollection() - Method in class io.seqware.webservice.generated.model.Registration
-
- getSampleCollection() - Method in class io.seqware.webservice.generated.model.Sample
-
- getSampleCollection1() - Method in class io.seqware.webservice.generated.model.Sample
-
- getSampleDescription() - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.SampleInfo
-
Get the value of sampleDescription
- getSampleHierarchies() - Method in class net.sourceforge.seqware.queryengine.webservice.model.SampleHierarchies
-
- getSampleHtml(Sample, Registration, String, String, boolean, boolean, String) - Static method in class net.sourceforge.solexatools.util.NodeHtmlUtil
-
getSampleHtml.
- getSampleHtml(Sample, Registration, Integer) - Static method in class net.sourceforge.solexatools.util.TreeNodeHtmlUtil
-
getSampleHtml.
- getSampleId() - Method in class io.seqware.webservice.generated.model.FileReport
-
- getSampleId() - Method in class io.seqware.webservice.generated.model.Ius
-
- getSampleId() - Method in class io.seqware.webservice.generated.model.Lane
-
- getSampleId() - Method in class io.seqware.webservice.generated.model.ProcessingSamples
-
- getSampleId() - Method in class io.seqware.webservice.generated.model.Sample
-
- getSampleId() - Method in class io.seqware.webservice.generated.model.SampleAttribute
-
- getSampleId() - Method in class io.seqware.webservice.generated.model.SampleLink
-
- getSampleId() - Method in class io.seqware.webservice.generated.model.SampleSearch
-
- getSampleId() - Method in class io.seqware.webservice.generated.model.SequencerRunAttribute
-
- getSampleId() - Method in class io.seqware.webservice.generated.model.ShareSample
-
- getSampleId() - Method in class net.sourceforge.seqware.common.model.Sample
-
Getter for the field
sampleId.
- getSampleId() - Method in class net.sourceforge.seqware.common.model.UploadSequence
-
Getter for the field sampleId.
- getSampleId() - Method in class net.sourceforge.seqware.queryengine.webservice.model.SampleHierarchy
-
- getSampleId() - Method in class net.sourceforge.seqware.webservice.dto.LibraryIdentityDto
-
Getter for the field sampleId.
- getSampleLinkCollection() - Method in class io.seqware.webservice.generated.model.Sample
-
- getSampleLinkId() - Method in class io.seqware.webservice.generated.model.SampleLink
-
- getSampleLinkId() - Method in class net.sourceforge.seqware.common.model.SampleLink
-
Getter for the field sampleLinkId.
- getSampleLinks() - Method in class net.sourceforge.seqware.common.model.Sample
-
Getter for the field
sampleLinks.
- getSampleName() - Method in class net.sourceforge.seqware.common.hibernate.SequencerRunReport.Row
-
- getSampleRelationshipCollection() - Method in class io.seqware.webservice.generated.model.Sample
-
- getSampleRelationshipCollection1() - Method in class io.seqware.webservice.generated.model.Sample
-
- getSampleRelationshipId() - Method in class io.seqware.webservice.generated.model.SampleRelationship
-
- getSampleReportService() - Method in class net.sourceforge.seqware.common.ContextImpl
-
Getter for the field sampleReportService.
- getSampleReportServiceBean() - Static method in class net.sourceforge.seqware.common.factory.BeanFactory
-
getSampleReportServiceBean.
- getSamples() - Method in class net.sourceforge.seqware.common.model.Experiment
-
Getter for the field samples.
- getSamples() - Method in class net.sourceforge.seqware.common.model.Lane
-
getSamples.
- getSamples() - Method in class net.sourceforge.seqware.common.model.Processing
-
Getter for the field samples.
- getSamples() - Method in class net.sourceforge.seqware.common.model.WorkflowRun
-
Getter for the field samples.
- getSamples() - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.LaneInfo
-
Get the value of samples
- getSampleSearch() - Method in class net.sourceforge.seqware.common.model.SampleSearchAttribute
-
Getter for the field sampleSearch.
- getSampleSearchAttributeCollection() - Method in class io.seqware.webservice.generated.model.SampleSearch
-
- getSampleSearchAttributeId() - Method in class io.seqware.webservice.generated.model.SampleSearchAttribute
-
- getSampleSearchAttributeId() - Method in class net.sourceforge.seqware.common.model.SampleSearchAttribute
-
Getter for the field sampleSearchAttributeId.
- getSampleSearchAttributes() - Method in class net.sourceforge.seqware.common.model.SampleSearch
-
Getter for the field sampleSearchAttributes.
- getSampleSearchCollection() - Method in class io.seqware.webservice.generated.model.Sample
-
- getSampleSearchId() - Method in class io.seqware.webservice.generated.model.SampleSearch
-
- getSampleSearchId() - Method in class io.seqware.webservice.generated.model.SampleSearchAttribute
-
- getSampleSearchId() - Method in class net.sourceforge.seqware.common.model.SampleSearch
-
Getter for the field sampleSearchId.
- getSampleSearchService() - Method in class net.sourceforge.seqware.common.ContextImpl
-
Getter for the field sampleSearchService.
- getSampleSearchServiceBean() - Static method in class net.sourceforge.seqware.common.factory.BeanFactory
-
getSampleSearchServiceBean.
- getSampleService() - Method in class net.sourceforge.seqware.common.ContextImpl
-
Getter for the field sampleService.
- getSampleService() - Method in class net.sourceforge.solexatools.validation.SampleValidator
-
Getter for the field sampleService.
- getSampleService() - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysBulkDownloadListDetailsController
-
Getter for the field sampleService.
- getSampleService() - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysListDetailsController
-
Getter for the field sampleService.
- getSampleService() - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysRunningListDetailsController
-
Getter for the field sampleService.
- getSampleService() - Method in class net.sourceforge.solexatools.webapp.controller.BulkDownloadListDetailsController
-
Getter for the field sampleService.
- getSampleService() - Method in class net.sourceforge.solexatools.webapp.controller.DownloadFileListController
-
Getter for the field sampleService.
- getSampleService() - Method in class net.sourceforge.solexatools.webapp.controller.LaneController
-
Getter for the field sampleService.
- getSampleService() - Method in class net.sourceforge.solexatools.webapp.controller.LaneSampleAssociateController
-
Getter for the field sampleService.
- getSampleService() - Method in class net.sourceforge.solexatools.webapp.controller.LaneSampleAssociateSetupController
-
Getter for the field sampleService.
- getSampleService() - Method in class net.sourceforge.solexatools.webapp.controller.LaunchWorkflowListDetailsController
-
Getter for the field sampleService.
- getSampleService() - Method in class net.sourceforge.solexatools.webapp.controller.SampleController
-
Getter for the field sampleService.
- getSampleService() - Method in class net.sourceforge.solexatools.webapp.controller.SampleSetupController
-
Getter for the field sampleService.
- getSampleService() - Method in class net.sourceforge.solexatools.webapp.controller.SaveOpenNodeController
-
Getter for the field sampleService.
- getSampleService() - Method in class net.sourceforge.solexatools.webapp.controller.SelectInputListController
-
Getter for the field sampleService.
- getSampleService() - Method in class net.sourceforge.solexatools.webapp.controller.StudyListDetailsController
-
Getter for the field sampleService.
- getSampleService() - Method in class net.sourceforge.solexatools.webapp.controller.StudyListDetailsFlatController
-
Getter for the field sampleService.
- getSampleService() - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileController
-
Getter for the field sampleService.
- getSampleService() - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileSetupController
-
Getter for the field sampleService.
- getSampleService() - Method in class net.sourceforge.solexatools.webapp.controller.UploadSequenceController
-
Getter for the field sampleService.
- getSampleService() - Method in class net.sourceforge.solexatools.webapp.controller.UploadSequenceSetupController
-
Getter for the field sampleService.
- getSampleServiceBean() - Static method in class net.sourceforge.seqware.common.factory.BeanFactory
-
getSampleServiceBean.
- getSamplesFrom(int) - Method in interface net.sourceforge.seqware.common.metadata.Metadata
-
Get the samples from an experiment.
- getSamplesFrom(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
-
- getSamplesFrom(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection
-
- getSamplesFrom(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS
-
- getSampleSwa() - Method in class net.sourceforge.seqware.common.hibernate.SequencerRunReport.Row
-
- getSampleSwas() - Method in class net.sourceforge.seqware.common.business.impl.ValidationReportServiceImpl.ReportEntry
-
- getSampleType() - Method in class net.sourceforge.seqware.common.model.Lane
-
Getter for the field sampleType.
- getSampleUrl() - Method in class net.sourceforge.seqware.webservice.dto.SampleSearchDto
-
Getter for the field sampleUrl.
- getScientificName() - Method in class io.seqware.webservice.generated.model.Sample
-
- getSelectedIds(HttpServletRequest, String, String[], String[]) - Static method in class net.sourceforge.solexatools.util.BulkUtil
-
getSelectedIds.
- getSelectedWorkflowParamValue(HttpServletRequest) - Static method in class net.sourceforge.solexatools.util.LaunchWorkflowUtil
-
getSelectedWorkflowParamValue.
- getSelection() - Method in class io.seqware.webservice.generated.model.ExperimentLibraryDesign
-
- getSelection() - Method in class net.sourceforge.seqware.common.model.ExperimentLibraryDesign
-
Getter for the field selection.
- getSender() - Method in class net.sourceforge.solexatools.webapp.controller.InviteNewUserController
-
Getter for the field sender.
- getSequencer_run_url() - Method in class net.sourceforge.seqware.webservice.dto.IusDto
-
Getter for the field sequencer_run_url.
- getSequencerRun(int) - Method in interface net.sourceforge.seqware.common.metadata.Metadata
-
getSequencerRun.
- getSequencerRun(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
-
- getSequencerRun(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection
-
- getSequencerRun(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS
-
- getSequencerRun() - Method in class net.sourceforge.seqware.common.model.Lane
-
Getter for the field sequencerRun.
- getSequencerRun() - Method in class net.sourceforge.seqware.common.model.ProcessingSequencerRuns
-
Getter for the field sequencerRun.
- getSequencerRun() - Method in class net.sourceforge.seqware.common.model.SampleReportRow
-
Getter for the field sequencerRun.
- getSequencerRun() - Method in class net.sourceforge.seqware.common.model.SequencerRunReportId
-
Getter for the field sequencerRun.
- getSequencerRun() - Method in class net.sourceforge.seqware.pipeline.plugins.filelinker.FileLinkerLine
-
- getSequencerRun(Lane) - Static method in class net.sourceforge.solexatools.util.FindRootUtil
-
getSequencerRun.
- getSequencerRun(Processing) - Static method in class net.sourceforge.solexatools.util.FindRootUtil
-
getSequencerRun.
- getSequencerRun() - Method in class net.sourceforge.solexatools.webapp.metamodel.SampleDetailsLineItem
-
Getter for the field sequencerRun.
- getSequencerRunAttributeCollection() - Method in class io.seqware.webservice.generated.model.SequencerRun
-
- getSequencerRunAttributeId() - Method in class io.seqware.webservice.generated.model.SequencerRunAttribute
-
- getSequencerRunAttributeId() - Method in class net.sourceforge.seqware.common.model.SequencerRunAttribute
-
Getter for the field sequencerRunAttributeId.
- getSequencerRunAttributes() - Method in class net.sourceforge.seqware.common.model.SequencerRun
-
Getter for the field sequencerRunAttributes.
- getSequencerRunByName(String) - Method in interface net.sourceforge.seqware.common.metadata.Metadata
-
- getSequencerRunByName(String) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
-
- getSequencerRunByName(String) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection
-
- getSequencerRunByName(String) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS
-
- getSequencerRunCollection() - Method in class io.seqware.webservice.generated.model.Platform
-
- getSequencerRunCollection() - Method in class io.seqware.webservice.generated.model.Registration
-
- getSequencerRunHtml(SequencerRun, Registration, String, String) - Static method in class net.sourceforge.solexatools.util.NodeHtmlUtil
-
getSequencerRunHtml.
- getSequencerRunId() - Method in class io.seqware.webservice.generated.model.Lane
-
- getSequencerRunId() - Method in class io.seqware.webservice.generated.model.ProcessingSequencerRuns
-
- getSequencerRunId() - Method in class io.seqware.webservice.generated.model.SampleReport
-
- getSequencerRunId() - Method in class io.seqware.webservice.generated.model.SequencerRun
-
- getSequencerRunId() - Method in class net.sourceforge.seqware.common.model.SequencerRun
-
Getter for the field sequencerRunId.
- getSequencerRunId() - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
-
Getter for the field sequencerRunId.
- getSequencerRunReport() - Method in interface net.sourceforge.seqware.common.metadata.Metadata
-
getSequencerRunReport.
- getSequencerRunReport() - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
-
getSequencerRunReport.
- getSequencerRunReport() - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection
-
getSequencerRunReport.
- getSequencerRunReport() - Method in class net.sourceforge.seqware.common.metadata.MetadataWS
-
getSequencerRunReport.
- getSequencerRunReportIds(SequencerRun, String, String, int, int) - Method in class net.sourceforge.seqware.common.business.impl.SampleReportServiceImpl
-
getSequencerRunReportIds.
- getSequencerRunReportIds(SequencerRun) - Method in class net.sourceforge.seqware.common.business.impl.SampleReportServiceImpl
-
getSequencerRunReportIds.
- getSequencerRunReportIds(SequencerRun, String, String) - Method in class net.sourceforge.seqware.common.business.impl.SampleReportServiceImpl
-
getSequencerRunReportIds.
- getSequencerRunReportIds(SequencerRun, String, String, int, int) - Method in interface net.sourceforge.seqware.common.business.SampleReportService
-
getSequencerRunReportIds.
- getSequencerRunReportIds(SequencerRun) - Method in interface net.sourceforge.seqware.common.business.SampleReportService
-
getSequencerRunReportIds.
- getSequencerRunReportIds(SequencerRun, String, String) - Method in interface net.sourceforge.seqware.common.business.SampleReportService
-
getSequencerRunReportIds.
- getSequencerRunReportIds(SequencerRun, String, String, int, int) - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleReportDAOHibernate
-
getSequencerRunReportIds.
- getSequencerRunReportIds(SequencerRun) - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleReportDAOHibernate
-
getSequencerRunReportIds.
- getSequencerRunReportIds(SequencerRun, String, String, int, int) - Method in interface net.sourceforge.seqware.common.dao.SampleReportDAO
-
getSequencerRunReportIds.
- getSequencerRunReportIds(SequencerRun) - Method in interface net.sourceforge.seqware.common.dao.SampleReportDAO
-
getSequencerRunReportIds.
- getSequencerRuns() - Method in class net.sourceforge.seqware.common.model.Processing
-
Getter for the field sequencerRuns.
- getSequencerRunService() - Method in class net.sourceforge.seqware.common.ContextImpl
-
Getter for the field sequencerRunService.
- getSequencerRunService() - Method in class net.sourceforge.solexatools.validation.SequencerRunValidator
-
Getter for the field sequencerRunService.
- getSequencerRunService() - Method in class net.sourceforge.solexatools.webapp.controller.ProcessingController
-
Getter for the field sequencerRunService.
- getSequencerRunService() - Method in class net.sourceforge.solexatools.webapp.controller.ProcessingSetupController
-
Getter for the field sequencerRunService.
- getSequencerRunService() - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunController
-
Getter for the field sequencerRunService.
- getSequencerRunService() - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunControllerDTO
-
Getter for the field sequencerRunService.
- getSequencerRunService() - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunListController
-
Getter for the field sequencerRunService.
- getSequencerRunService() - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunListDetailsController
-
Getter for the field sequencerRunService.
- getSequencerRunService() - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunSetupController
-
Getter for the field sequencerRunService.
- getSequencerRunService() - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunSetupControllerDTO
-
Getter for the field sequencerRunService.
- getSequencerRunService() - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunWizardController
-
Getter for the field sequencerRunService.
- getSequencerRunService() - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunWizardSetupController
-
Getter for the field sequencerRunService.
- getSequencerRunService() - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileController
-
Getter for the field sequencerRunService.
- getSequencerRunService() - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileSetupController
-
Getter for the field sequencerRunService.
- getSequencerRunService() - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowRunController
-
Getter for the field sequencerRunService.
- getSequencerRunServiceBean() - Static method in class net.sourceforge.seqware.common.factory.BeanFactory
-
getSequencerRunServiceBean.
- getSequencerRunSwas() - Method in class net.sourceforge.seqware.common.business.impl.ValidationReportServiceImpl.ReportEntry
-
- getSequencerRunValidator() - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunWizardController
-
Getter for the field sequencerRunValidator.
- getSequencerRunWizardDTO() - Method in class net.sourceforge.seqware.common.model.SequencerRunAttribute
-
getSequencerRunWizardDTO.
- getSequencerRunWizardValidator() - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunWizardController
-
Getter for the field sequencerRunWizardValidator.
- getSequenceSpace() - Method in class io.seqware.webservice.generated.model.Experiment
-
- getSequenceSpace() - Method in class net.sourceforge.seqware.common.model.Experiment
-
Getter for the field sequenceSpace.
- getSEQWARE_DB() - Method in class net.sourceforge.seqware.common.util.testtools.BasicTestDatabaseCreator
-
- getSEQWARE_DB() - Method in class net.sourceforge.seqware.metadb.util.TestDatabaseCreator
-
- getSEQWARE_DB() - Method in class net.sourceforge.seqware.pipeline.plugins.ExtendedTestDatabaseCreator
-
- getSEQWARE_PASSWORD() - Method in class net.sourceforge.seqware.common.util.testtools.BasicTestDatabaseCreator
-
- getSEQWARE_PASSWORD() - Method in class net.sourceforge.seqware.metadb.util.TestDatabaseCreator
-
- getSEQWARE_PASSWORD() - Method in class net.sourceforge.seqware.pipeline.plugins.ExtendedTestDatabaseCreator
-
- getSEQWARE_USER() - Method in class net.sourceforge.seqware.common.util.testtools.BasicTestDatabaseCreator
-
- getSEQWARE_USER() - Method in class net.sourceforge.seqware.metadb.util.TestDatabaseCreator
-
- getSEQWARE_USER() - Method in class net.sourceforge.seqware.pipeline.plugins.ExtendedTestDatabaseCreator
-
- getSeqware_version() - Method in class net.sourceforge.seqware.pipeline.workflowV2.AbstractWorkflowDataModel
-
- getSeqwareAccession() - Method in class net.sourceforge.seqware.pipeline.plugins.filelinker.FileLinkerLine
-
- getSeqwareRevision() - Method in class io.seqware.webservice.generated.model.WorkflowRun
-
- getSeqwareRevision() - Method in class net.sourceforge.seqware.common.model.WorkflowRun
-
Getter for the field seqwareRevision.
- getSeqwareVersion() - Method in class io.seqware.webservice.generated.model.Workflow
-
- getSeqwareVersion() - Method in class net.sourceforge.seqware.common.model.Workflow
-
Getter for the field seqwareVersion.
- getSerialVersionUID() - Static method in class net.sourceforge.seqware.common.model.Experiment
-
Getter for the field serialVersionUID.
- getSerialVersionUID() - Static method in class net.sourceforge.seqware.common.model.ExperimentLibraryDesign
-
Getter for the field serialVersionUID.
- getSerialVersionUID() - Static method in class net.sourceforge.seqware.common.model.ExperimentSpotDesign
-
Getter for the field serialVersionUID.
- getSerialVersionUID() - Static method in class net.sourceforge.seqware.common.model.Lane
-
Getter for the field serialVersionUID.
- getSerialVersionUID() - Static method in class net.sourceforge.seqware.common.model.Platform
-
Getter for the field serialVersionUID.
- getSerialVersionUID() - Static method in class net.sourceforge.seqware.common.model.Processing
-
Getter for the field serialVersionUID.
- getSerialVersionUID() - Static method in class net.sourceforge.seqware.common.model.Sample
-
Getter for the field
serialVersionUID.
- getSerialVersionUID() - Static method in class net.sourceforge.seqware.common.model.SequencerRun
-
Getter for the field serialVersionUID.
- getSerialVersionUID() - Static method in class net.sourceforge.seqware.common.model.SequencerRunDTO
-
Getter for the field serialVersionUID.
- getSerialVersionUID() - Static method in class net.sourceforge.seqware.common.model.Study
-
Getter for the field serialVersionUID.
- getSerialVersionUID() - Static method in class net.sourceforge.seqware.common.model.StudyType
-
Getter for the field serialVersionUID.
- getSessionFactory() - Method in class net.sourceforge.seqware.common.ContextImpl
-
Getter for the field sessionFactory.
- getSessionFactoryBean() - Static method in class net.sourceforge.seqware.common.factory.BeanFactory
-
getSessionFactoryBean.
- getSettings() - Static method in class net.sourceforge.seqware.common.util.configtools.ConfigTools
-
The output keys are always uppercase!
- getSettingsFilePath() - Static method in class net.sourceforge.seqware.common.util.configtools.ConfigTools
-
- getSharedStudies() - Method in class net.sourceforge.seqware.common.model.Study
-
Getter for the field sharedStudies.
- getSharedWorkflowRuns() - Method in class net.sourceforge.seqware.common.model.WorkflowRun
-
Getter for the field sharedWorkflowRuns.
- getShareExperimentCollection() - Method in class io.seqware.webservice.generated.model.Experiment
-
- getShareExperimentCollection() - Method in class io.seqware.webservice.generated.model.Registration
-
- getShareExperimentId() - Method in class io.seqware.webservice.generated.model.ShareExperiment
-
- getShareExperimentId() - Method in class net.sourceforge.seqware.common.model.ShareExperiment
-
Getter for the field shareExperimentId.
- getShareFileCollection() - Method in class io.seqware.webservice.generated.model.File
-
- getShareFileCollection() - Method in class io.seqware.webservice.generated.model.Registration
-
- getShareFileId() - Method in class io.seqware.webservice.generated.model.ShareFile
-
- getShareFileId() - Method in class net.sourceforge.seqware.common.model.ShareFile
-
Getter for the field shareFileId.
- getShareLaneCollection() - Method in class io.seqware.webservice.generated.model.Lane
-
- getShareLaneCollection() - Method in class io.seqware.webservice.generated.model.Registration
-
- getShareLaneId() - Method in class io.seqware.webservice.generated.model.ShareLane
-
- getShareLaneId() - Method in class net.sourceforge.seqware.common.model.ShareLane
-
Getter for the field shareLaneId.
- getShareProcessingCollection() - Method in class io.seqware.webservice.generated.model.Processing
-
- getShareProcessingCollection() - Method in class io.seqware.webservice.generated.model.Registration
-
- getShareProcessingId() - Method in class io.seqware.webservice.generated.model.ShareProcessing
-
- getShareProcessingId() - Method in class net.sourceforge.seqware.common.model.ShareProcessing
-
Getter for the field shareProcessingId.
- getShareSampleCollection() - Method in class io.seqware.webservice.generated.model.Registration
-
- getShareSampleCollection() - Method in class io.seqware.webservice.generated.model.Sample
-
- getShareSampleId() - Method in class io.seqware.webservice.generated.model.ShareSample
-
- getShareSampleId() - Method in class net.sourceforge.seqware.common.model.ShareSample
-
Getter for the field shareSampleId.
- getShareStudyCollection() - Method in class io.seqware.webservice.generated.model.Registration
-
- getShareStudyCollection() - Method in class io.seqware.webservice.generated.model.Study
-
- getShareStudyId() - Method in class io.seqware.webservice.generated.model.ShareStudy
-
- getShareStudyId() - Method in class net.sourceforge.seqware.common.model.ShareStudy
-
Getter for the field shareStudyId.
- getShareStudyService() - Method in class net.sourceforge.solexatools.webapp.controller.ShareValidatorController
-
Getter for the field shareStudyService.
- getShareStudyService() - Method in class net.sourceforge.solexatools.webapp.controller.StudyController
-
Getter for the field shareStudyService.
- getShareWorkflowRun(String, WorkflowRun) - Method in class net.sourceforge.seqware.common.dao.hibernate.ShareWorkflowRunDAOHibernate
-
getShareWorkflowRun.
- getShareWorkflowRun(String, WorkflowRun) - Method in interface net.sourceforge.seqware.common.dao.ShareWorkflowRunDAO
-
getShareWorkflowRun.
- getShareWorkflowRunCollection() - Method in class io.seqware.webservice.generated.model.Registration
-
- getShareWorkflowRunCollection() - Method in class io.seqware.webservice.generated.model.WorkflowRun
-
- getShareWorkflowRunId() - Method in class io.seqware.webservice.generated.model.ShareWorkflowRun
-
- getShareWorkflowRunId() - Method in class net.sourceforge.seqware.common.model.ShareWorkflowRun
-
Getter for the field shareWorkflowRunId.
- getShareWorkflowRunService() - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysEventController
-
Getter for the field shareWorkflowRunService.
- getShareWorkflowRunService() - Method in class net.sourceforge.solexatools.webapp.controller.ShareValidatorController
-
Getter for the field shareWorkflowRunService.
- getSingleWorkflowRun(Integer) - Method in class net.sourceforge.seqware.common.hibernate.WorkflowRunReport
-
Using a workflow run SWID, report on the files, samples and processing
events associated with the run.
- getSite() - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object.Pfn
-
Getter for the field site.
- getSize() - Method in class io.seqware.webservice.generated.model.File
-
- getSize() - Method in class net.sourceforge.seqware.common.model.File
-
Getter for the field size.
- getSize() - Method in class net.sourceforge.seqware.common.module.FileMetadata
-
- getSize() - Method in class net.sourceforge.seqware.pipeline.plugins.filelinker.FileLinkerLine
-
- getSize() - Method in class net.sourceforge.seqware.webservice.dto.FileDto
-
Getter for the field size.
- getSkip() - Method in class io.seqware.webservice.generated.model.File
-
- getSkip() - Method in class io.seqware.webservice.generated.model.Ius
-
- getSkip() - Method in class io.seqware.webservice.generated.model.Lane
-
- getSkip() - Method in class io.seqware.webservice.generated.model.Sample
-
- getSkip() - Method in class io.seqware.webservice.generated.model.SequencerRun
-
- getSkip() - Method in class net.sourceforge.seqware.common.model.File
-
- getSkip() - Method in class net.sourceforge.seqware.common.model.IUS
-
Getter for the field skip.
- getSkip() - Method in class net.sourceforge.seqware.common.model.Lane
-
Getter for the field skip.
- getSkip() - Method in class net.sourceforge.seqware.common.model.Sample
-
Getter for the field
skip.
- getSkip() - Method in class net.sourceforge.seqware.common.model.SequencerRun
-
Getter for the field skip.
- getSkip() - Method in class net.sourceforge.seqware.webservice.dto.IusDto
-
Getter for the field skip.
- getSlide1FilePath() - Method in class io.seqware.webservice.generated.model.SequencerRun
-
- getSlide1LaneCount() - Method in class io.seqware.webservice.generated.model.SequencerRun
-
- getSlide2FilePath() - Method in class io.seqware.webservice.generated.model.SequencerRun
-
- getSlide2LaneCount() - Method in class io.seqware.webservice.generated.model.SequencerRun
-
- getSlideCount() - Method in class io.seqware.webservice.generated.model.SequencerRun
-
- getSlideOneFilePath() - Method in class net.sourceforge.seqware.common.model.SequencerRun
-
Getter for the field slideOneFilePath.
- getSlideOneFilePath() - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
-
Getter for the field slideOneFilePath.
- getSlideOneLaneCount() - Method in class net.sourceforge.seqware.common.model.SequencerRun
-
Getter for the field slideOneLaneCount.
- getSlideOneLaneCount() - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
-
Getter for the field slideOneLaneCount.
- getSlideTwoFilePath() - Method in class net.sourceforge.seqware.common.model.SequencerRun
-
Getter for the field slideTwoFilePath.
- getSlideTwoFilePath() - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
-
Getter for the field slideTwoFilePath.
- getSlideTwoLaneCount() - Method in class net.sourceforge.seqware.common.model.SequencerRun
-
Getter for the field slideTwoLaneCount.
- getSlideTwoLaneCount() - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
-
Getter for the field slideTwoLaneCount.
- getSortKeySample() - Method in class net.sourceforge.solexatools.webapp.metamodel.StudySampleReportLineItem
-
Getter for the field sortKeySample.
- getSource() - Method in class io.seqware.webservice.generated.model.ExperimentLibraryDesign
-
- getSource() - Method in class net.sourceforge.seqware.common.model.ExperimentLibraryDesign
-
Getter for the field source.
- getSourcePath() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.SqwFile
-
- getSourceReader(String, int, long) - Method in class net.sourceforge.seqware.common.util.filetools.ProvisionFilesUtil
-
This attempts to resume if passed in startPosition > 0.
- getSpotDesignReadSpec() - Method in class net.sourceforge.seqware.common.model.Experiment
-
Getter for the field spotDesignReadSpec.
- getSql() - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
-
Getter for the field
sql.
- getStartDate() - Method in class io.seqware.webservice.generated.model.Invoice
-
- getStartDate() - Method in class net.sourceforge.seqware.common.model.Invoice
-
Getter for the field startDate.
- getStartPage() - Method in class net.sourceforge.solexatools.util.PageInfo
-
Getter for the field startPage.
- getState() - Method in class io.seqware.webservice.generated.model.Invoice
-
- getState() - Method in class net.sourceforge.seqware.common.model.Invoice
-
Getter for the field state.
- getStatus() - Method in class io.seqware.webservice.generated.model.Experiment
-
- getStatus() - Method in class io.seqware.webservice.generated.model.Processing
-
- getStatus() - Method in class io.seqware.webservice.generated.model.SampleReport
-
- getStatus() - Method in class io.seqware.webservice.generated.model.SequencerRun
-
- getStatus() - Method in class io.seqware.webservice.generated.model.Study
-
- getStatus() - Method in class io.seqware.webservice.generated.model.WorkflowRun
-
- getStatus(Study, Sample, Workflow) - Method in class net.sourceforge.seqware.common.business.impl.SampleReportServiceImpl
-
getStatus.
- getStatus(Study, Sample, IUS, Lane, SequencerRun, Workflow) - Method in class net.sourceforge.seqware.common.business.impl.SampleReportServiceImpl
-
getStatus.
- getStatus(Study, Sample, Workflow) - Method in interface net.sourceforge.seqware.common.business.SampleReportService
-
getStatus.
- getStatus(Study, Sample, IUS, Lane, SequencerRun, Workflow) - Method in interface net.sourceforge.seqware.common.business.SampleReportService
-
getStatus.
- getStatus(Study, Sample, Workflow) - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleReportDAOHibernate
-
getStatus.
- getStatus(Study, Sample, IUS, Lane, SequencerRun, Workflow) - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleReportDAOHibernate
-
getStatus.
- getStatus(Study, Sample, Workflow) - Method in interface net.sourceforge.seqware.common.dao.SampleReportDAO
-
getStatus.
- getStatus(Study, Sample, IUS, Lane, SequencerRun, Workflow) - Method in interface net.sourceforge.seqware.common.dao.SampleReportDAO
-
getStatus.
- getStatus() - Method in class net.sourceforge.seqware.common.model.Experiment
-
Getter for the field status.
- getStatus() - Method in class net.sourceforge.seqware.common.model.Processing
-
- getStatus() - Method in class net.sourceforge.seqware.common.model.SampleReportRow
-
Getter for the field status.
- getStatus() - Method in class net.sourceforge.seqware.common.model.SequencerRun
-
Getter for the field status.
- getStatus() - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
-
Getter for the field status.
- getStatus() - Method in class net.sourceforge.seqware.common.model.Study
-
Getter for the field status.
- getStatus() - Method in class net.sourceforge.seqware.common.model.WorkflowRun
-
Getter for the field status.
- getStatus() - Method in enum net.sourceforge.seqware.common.module.ReturnValue.ExitStatus
-
- getStatus() - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.RunInfo
-
Get the value of the sequencer run status
- getStatusCmd() - Method in class io.seqware.webservice.generated.model.WorkflowRun
-
- getStatusCmd() - Method in class net.sourceforge.seqware.common.model.WorkflowRun
-
Getter for the field statusCmd.
- getStatusCount(Study, WorkflowRunStatus) - Method in class net.sourceforge.seqware.common.dao.hibernate.StudyDAOHibernate
-
Count the number of workflow runs with the given status, under the given study
- getStatusCount(Study, WorkflowRunStatus) - Method in interface net.sourceforge.seqware.common.dao.StudyDAO
-
Count the number of workflow runs with the given status, under the given study
- getStatusCounts() - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowTools
-
Getter for the field statusCounts.
- getStatuses() - Method in class net.sourceforge.solexatools.webapp.metamodel.StudySampleReportLineItem
-
Getter for the field statuses.
- getStatusesForSequencerRun(SequencerRun) - Method in class net.sourceforge.seqware.common.business.impl.SampleReportServiceImpl
-
getStatusesForSequencerRun.
- getStatusesForSequencerRun(SequencerRun) - Method in interface net.sourceforge.seqware.common.business.SampleReportService
-
getStatusesForSequencerRun.
- getStatusesForSequencerRun(SequencerRun) - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleReportDAOHibernate
-
getStatusesForSequencerRun.
- getStatusesForSequencerRun(SequencerRun) - Method in interface net.sourceforge.seqware.common.dao.SampleReportDAO
-
getStatusesForSequencerRun.
- getStatusesForStudy(Study) - Method in class net.sourceforge.seqware.common.business.impl.SampleReportServiceImpl
-
getStatusesForStudy.
- getStatusesForStudy(Study) - Method in interface net.sourceforge.seqware.common.business.SampleReportService
-
getStatusesForStudy.
- getStatusesForStudy(Study) - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleReportDAOHibernate
-
getStatusesForStudy.
- getStatusesForStudy(Study) - Method in interface net.sourceforge.seqware.common.dao.SampleReportDAO
-
getStatusesForStudy.
- getStatusesForWorkflow(Study, Workflow) - Method in class net.sourceforge.seqware.common.business.impl.SampleReportServiceImpl
-
getStatusesForWorkflow.
- getStatusesForWorkflow(SequencerRun, Workflow) - Method in class net.sourceforge.seqware.common.business.impl.SampleReportServiceImpl
-
getStatusesForWorkflow.
- getStatusesForWorkflow(Study, Workflow) - Method in interface net.sourceforge.seqware.common.business.SampleReportService
-
getStatusesForWorkflow.
- getStatusesForWorkflow(SequencerRun, Workflow) - Method in interface net.sourceforge.seqware.common.business.SampleReportService
-
getStatusesForWorkflow.
- getStatusesForWorkflow(Study, Workflow) - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleReportDAOHibernate
-
getStatusesForWorkflow.
- getStatusesForWorkflow(SequencerRun, Workflow) - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleReportDAOHibernate
-
getStatusesForWorkflow.
- getStatusesForWorkflow(Study, Workflow) - Method in interface net.sourceforge.seqware.common.dao.SampleReportDAO
-
getStatusesForWorkflow.
- getStatusesForWorkflow(SequencerRun, Workflow) - Method in interface net.sourceforge.seqware.common.dao.SampleReportDAO
-
getStatusesForWorkflow.
- getStderr() - Method in class io.seqware.webservice.generated.model.Processing
-
- getStderr() - Method in class io.seqware.webservice.generated.model.WorkflowRun
-
- getStderr() - Method in class net.sourceforge.seqware.common.model.Processing
-
Getter for the field stderr.
- getStdErr() - Method in class net.sourceforge.seqware.common.model.WorkflowRun
-
Getter for the field stdErr.
- getStderr() - Method in class net.sourceforge.seqware.common.module.ReturnValue
-
Getter for the field stderr.
- getStderrFile() - Method in class net.sourceforge.seqware.pipeline.module.Module
-
Getter for the file where the stderr will be redirected.
- getStdout() - Method in class io.seqware.webservice.generated.model.Processing
-
- getStdout() - Method in class io.seqware.webservice.generated.model.WorkflowRun
-
- getStdout() - Method in class net.sourceforge.seqware.common.model.Processing
-
Getter for the field stdout.
- getStdOut() - Method in class net.sourceforge.seqware.common.model.WorkflowRun
-
Getter for the field stdOut.
- getStdout() - Method in class net.sourceforge.seqware.common.module.ReturnValue
-
Getter for the field stdout.
- getStdoutFile() - Method in class net.sourceforge.seqware.pipeline.module.Module
-
Getter for the file where the stdout will be redirected.
- getStrategy() - Method in class io.seqware.webservice.generated.model.ExperimentLibraryDesign
-
- getStrategy() - Method in class net.sourceforge.seqware.common.model.ExperimentLibraryDesign
-
Getter for the field strategy.
- getStrExpectedNumberReads() - Method in class net.sourceforge.seqware.common.model.Experiment
-
Getter for the field strExpectedNumberReads.
- getStrExpectedNumberRuns() - Method in class net.sourceforge.seqware.common.model.Experiment
-
Getter for the field strExpectedNumberRuns.
- getStrExpectedNumReads() - Method in class net.sourceforge.seqware.common.model.Sample
-
Getter for the field
strExpectedNumReads.
- getStrExpectedNumRuns() - Method in class net.sourceforge.seqware.common.model.Sample
-
Getter for the field
strExpectedNumRuns.
- getStrLaneCount() - Method in class net.sourceforge.seqware.common.model.SequencerRunWizardDTO
-
Getter for the field strLaneCount.
- getStrRefLane() - Method in class net.sourceforge.seqware.common.model.SequencerRun
-
Getter for the field strRefLane.
- getStrStartURL() - Method in class net.sourceforge.seqware.common.business.UploadFile
-
Getter for the field strStartURL.
- getStrStartURL() - Method in class net.sourceforge.seqware.common.model.UploadSequence
-
Getter for the field strStartURL.
- getStudies() - Method in class net.sourceforge.seqware.common.model.Processing
-
Getter for the field studies.
- getStudy() - Method in class net.sourceforge.seqware.common.model.Experiment
-
Getter for the field study.
- getStudy() - Method in class net.sourceforge.seqware.common.model.FileReportRow
-
Getter for the field study.
- getStudy() - Method in class net.sourceforge.seqware.common.model.ProcessingStudies
-
Getter for the field study.
- getStudy() - Method in class net.sourceforge.seqware.common.model.SampleReportRow
-
Getter for the field study.
- getStudy() - Method in class net.sourceforge.seqware.common.model.SequencerRunReportId
-
Getter for the field study.
- getStudy() - Method in class net.sourceforge.seqware.common.model.StudyAttribute
-
Getter for the field study.
- getStudy() - Method in class net.sourceforge.seqware.common.model.StudyLink
-
Getter for the field study.
- getStudy(Experiment) - Static method in class net.sourceforge.solexatools.util.FindRootUtil
-
getStudy.
- getStudy(Sample) - Static method in class net.sourceforge.solexatools.util.FindRootUtil
-
getStudy.
- getStudy(Lane) - Static method in class net.sourceforge.solexatools.util.FindRootUtil
-
getStudy.
- getStudy(Processing) - Static method in class net.sourceforge.solexatools.util.FindRootUtil
-
getStudy.
- getStudyAttributeCollection() - Method in class io.seqware.webservice.generated.model.Study
-
- getStudyAttributeId() - Method in class io.seqware.webservice.generated.model.StudyAttribute
-
- getStudyAttributeId() - Method in class net.sourceforge.seqware.common.model.StudyAttribute
-
Getter for the field studyAttributeId.
- getStudyAttributes() - Method in class net.sourceforge.seqware.common.model.Study
-
Getter for the field studyAttributes.
- getStudyAttributes() - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.RunInfo
-
Get the value of studyAttributes
- getStudyByName(String) - Method in interface net.sourceforge.seqware.common.metadata.Metadata
-
- getStudyByName(String) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
-
- getStudyByName(String) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection
-
- getStudyByName(String) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS
-
- getStudyCenterName() - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.RunInfo
-
Get the value of studyCenterName
- getStudyCenterProject() - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.RunInfo
-
Get the value of studyCenterProject
- getStudyCollection() - Method in class io.seqware.webservice.generated.model.Registration
-
- getStudyCollection() - Method in class io.seqware.webservice.generated.model.StudyType
-
- getStudyDAO() - Method in class net.sourceforge.seqware.common.business.impl.StudyServiceImpl
-
Getter for the field studyDAO.
- getStudyDescription() - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.RunInfo
-
Get the value of studyDescription
- getStudyId() - Method in class io.seqware.webservice.generated.model.Experiment
-
- getStudyId() - Method in class io.seqware.webservice.generated.model.FileReport
-
- getStudyId() - Method in class io.seqware.webservice.generated.model.ProcessingStudies
-
- getStudyId() - Method in class io.seqware.webservice.generated.model.SampleReport
-
- getStudyId() - Method in class io.seqware.webservice.generated.model.ShareStudy
-
- getStudyId() - Method in class io.seqware.webservice.generated.model.Study
-
- getStudyId() - Method in class io.seqware.webservice.generated.model.StudyAttribute
-
- getStudyId() - Method in class io.seqware.webservice.generated.model.StudyLink
-
- getStudyId() - Method in class net.sourceforge.seqware.common.model.ShareStudy
-
Getter for the field studyId.
- getStudyId() - Method in class net.sourceforge.seqware.common.model.Study
-
Getter for the field studyId.
- getStudyLinkCollection() - Method in class io.seqware.webservice.generated.model.Study
-
- getStudyLinkId() - Method in class io.seqware.webservice.generated.model.StudyLink
-
- getStudyLinkId() - Method in class net.sourceforge.seqware.common.model.StudyLink
-
Getter for the field studyLinkId.
- getStudyLinks() - Method in class net.sourceforge.seqware.common.model.Study
-
Getter for the field studyLinks.
- getStudyService() - Method in class net.sourceforge.seqware.common.ContextImpl
-
Getter for the field studyService.
- getStudyService() - Method in class net.sourceforge.solexatools.validation.StudyValidator
-
Getter for the field studyService.
- getStudyService() - Method in class net.sourceforge.solexatools.webapp.controller.BulkDownloadListController
-
Getter for the field studyService.
- getStudyService() - Method in class net.sourceforge.solexatools.webapp.controller.BulkDownloadListDetailsController
-
Getter for the field studyService.
- getStudyService() - Method in class net.sourceforge.solexatools.webapp.controller.DownloadFileListController
-
Getter for the field studyService.
- getStudyService() - Method in class net.sourceforge.solexatools.webapp.controller.ExperimentController
-
Getter for the field studyService.
- getStudyService() - Method in class net.sourceforge.solexatools.webapp.controller.ExperimentSetupController
-
Getter for the field studyService.
- getStudyService() - Method in class net.sourceforge.solexatools.webapp.controller.LaunchWorkflowListController
-
Getter for the field studyService.
- getStudyService() - Method in class net.sourceforge.solexatools.webapp.controller.LaunchWorkflowListDetailsController
-
Getter for the field studyService.
- getStudyService() - Method in class net.sourceforge.solexatools.webapp.controller.SelectInputListController
-
Getter for the field studyService.
- getStudyService() - Method in class net.sourceforge.solexatools.webapp.controller.ShareValidatorController
-
Getter for the field studyService.
- getStudyService() - Method in class net.sourceforge.solexatools.webapp.controller.StudyController
-
Getter for the field studyService.
- getStudyService() - Method in class net.sourceforge.solexatools.webapp.controller.StudyListController
-
Getter for the field studyService.
- getStudyService() - Method in class net.sourceforge.solexatools.webapp.controller.StudyListDetailsController
-
Getter for the field studyService.
- getStudyService() - Method in class net.sourceforge.solexatools.webapp.controller.StudyListDetailsFlatController
-
Getter for the field studyService.
- getStudyService() - Method in class net.sourceforge.solexatools.webapp.controller.StudyReportController
-
Getter for the field studyService.
- getStudyService() - Method in class net.sourceforge.solexatools.webapp.controller.StudySetupController
-
Getter for the field studyService.
- getStudyService() - Method in class net.sourceforge.solexatools.webapp.controller.StudyTableController
-
- getStudyService() - Method in class net.sourceforge.solexatools.webapp.controller.StudyTableControllerDetails
-
Getter for the field
studyService.
- getStudyService() - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileController
-
Getter for the field studyService.
- getStudyService() - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileSetupController
-
Getter for the field studyService.
- getStudyServiceBean() - Static method in class net.sourceforge.seqware.common.factory.BeanFactory
-
getStudyServiceBean.
- getStudySwas() - Method in class net.sourceforge.seqware.common.business.impl.ValidationReportServiceImpl.ReportEntry
-
- getStudyTitle() - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.RunInfo
-
Get the value of studyTitle
- getStudyType() - Method in class io.seqware.webservice.generated.model.Lane
-
- getStudyType() - Method in class net.sourceforge.seqware.common.model.Lane
-
- getStudyType() - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.RunInfo
-
- getStudyTypeAcc() - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.LaneInfo
-
Get the value of studyTypeAcc
- getStudyTypeDAO() - Method in class net.sourceforge.seqware.common.business.impl.StudyServiceImpl
-
Getter for the field studyTypeDAO.
- getStudyTypeId() - Method in class io.seqware.webservice.generated.model.StudyType
-
- getStudyTypeId() - Method in class net.sourceforge.seqware.common.model.StudyType
-
Getter for the field studyTypeId.
- getStudyTypes() - Method in interface net.sourceforge.seqware.common.metadata.Metadata
-
getStudyTypes.
- getStudyTypes() - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
-
- getStudyTypes() - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection
-
- getStudyTypes() - Method in class net.sourceforge.seqware.common.metadata.MetadataWS
-
- getStudyTypeService() - Method in class net.sourceforge.seqware.common.ContextImpl
-
- getStudyTypeService() - Method in class net.sourceforge.solexatools.webapp.controller.StudyController
-
Getter for the field studyTypeService.
- getStudyTypeService() - Method in class net.sourceforge.solexatools.webapp.controller.StudySetupController
-
Getter for the field studyTypeService.
- getStudyTypeServiceBean() - Static method in class net.sourceforge.seqware.common.factory.BeanFactory
-
getStudyTypeServiceBean.
- getStydyHtml(Study, Registration, String, boolean, String) - Static method in class net.sourceforge.solexatools.util.NodeHtmlUtil
-
getStydyHtml.
- getStydyHtml(Study, Registration, Integer, String) - Static method in class net.sourceforge.solexatools.util.TreeNodeHtmlUtil
-
getStydyHtml.
- getSubject(String, String, String) - Method in class net.sourceforge.solexatools.authentication.UNCKerberos
-
getSubject.
- getSubjectEmail() - Method in class net.sourceforge.seqware.common.invitation.InvitationParams
-
Getter for the field subjectEmail.
- getSummaryData(HttpServletRequest) - Static method in class net.sourceforge.solexatools.util.LaunchWorkflowUtil
-
getSummaryData.
- getSummaryLines() - Method in class net.sourceforge.solexatools.util.SummaryData
-
Getter for the field summaryLines.
- getSwa() - Method in class net.sourceforge.seqware.webservice.dto.IusDto
-
Getter for the field swa.
- getSwAccession() - Method in class io.seqware.webservice.generated.model.Expense
-
- getSwAccession() - Method in class io.seqware.webservice.generated.model.Experiment
-
- getSwAccession() - Method in class io.seqware.webservice.generated.model.File
-
- getSwAccession() - Method in class io.seqware.webservice.generated.model.Invoice
-
- getSwAccession() - Method in class io.seqware.webservice.generated.model.Ius
-
- getSwAccession() - Method in class io.seqware.webservice.generated.model.Lane
-
- getSwAccession() - Method in class io.seqware.webservice.generated.model.Processing
-
- getSwAccession() - Method in class io.seqware.webservice.generated.model.ProcessingExperiments
-
- getSwAccession() - Method in class io.seqware.webservice.generated.model.ProcessingIus
-
- getSwAccession() - Method in class io.seqware.webservice.generated.model.ProcessingLanes
-
- getSwAccession() - Method in class io.seqware.webservice.generated.model.ProcessingSamples
-
- getSwAccession() - Method in class io.seqware.webservice.generated.model.ProcessingSequencerRuns
-
- getSwAccession() - Method in class io.seqware.webservice.generated.model.ProcessingStudies
-
- getSwAccession() - Method in class io.seqware.webservice.generated.model.Sample
-
- getSwAccession() - Method in class io.seqware.webservice.generated.model.SequencerRun
-
- getSwAccession() - Method in class io.seqware.webservice.generated.model.ShareExperiment
-
- getSwAccession() - Method in class io.seqware.webservice.generated.model.ShareFile
-
- getSwAccession() - Method in class io.seqware.webservice.generated.model.ShareLane
-
- getSwAccession() - Method in class io.seqware.webservice.generated.model.ShareProcessing
-
- getSwAccession() - Method in class io.seqware.webservice.generated.model.ShareSample
-
- getSwAccession() - Method in class io.seqware.webservice.generated.model.ShareStudy
-
- getSwAccession() - Method in class io.seqware.webservice.generated.model.ShareWorkflowRun
-
- getSwAccession() - Method in class io.seqware.webservice.generated.model.Study
-
- getSwAccession() - Method in class io.seqware.webservice.generated.model.Workflow
-
- getSwAccession() - Method in class io.seqware.webservice.generated.model.WorkflowRun
-
- getSwAccession() - Method in class net.sourceforge.seqware.common.model.Expense
-
Getter for the field
swAccession.
- getSwAccession() - Method in class net.sourceforge.seqware.common.model.Experiment
-
Getter for the field swAccession.
- getSwAccession() - Method in class net.sourceforge.seqware.common.model.File
-
Getter for the field swAccession.
- getSwAccession() - Method in class net.sourceforge.seqware.common.model.Invoice
-
Getter for the field swAccession.
- getSwAccession() - Method in class net.sourceforge.seqware.common.model.IUS
-
Getter for the field swAccession.
- getSwAccession() - Method in class net.sourceforge.seqware.common.model.Lane
-
Getter for the field swAccession.
- getSwAccession() - Method in class net.sourceforge.seqware.common.model.Processing
-
Getter for the field swAccession.
- getSwAccession() - Method in class net.sourceforge.seqware.common.model.ProcessingExperiments
-
Getter for the field swAccession.
- getSwAccession() - Method in class net.sourceforge.seqware.common.model.ProcessingIus
-
Getter for the field swAccession.
- getSwAccession() - Method in class net.sourceforge.seqware.common.model.ProcessingLanes
-
Getter for the field swAccession.
- getSwAccession() - Method in class net.sourceforge.seqware.common.model.ProcessingSamples
-
Getter for the field swAccession.
- getSwAccession() - Method in class net.sourceforge.seqware.common.model.ProcessingSequencerRuns
-
Getter for the field swAccession.
- getSwAccession() - Method in class net.sourceforge.seqware.common.model.ProcessingStudies
-
Getter for the field swAccession.
- getSwAccession() - Method in class net.sourceforge.seqware.common.model.Sample
-
Getter for the field
swAccession.
- getSwAccession() - Method in class net.sourceforge.seqware.common.model.SequencerRun
-
Getter for the field swAccession.
- getSwAccession() - Method in class net.sourceforge.seqware.common.model.ShareExperiment
-
Getter for the field swAccession.
- getSwAccession() - Method in class net.sourceforge.seqware.common.model.ShareFile
-
Getter for the field swAccession.
- getSwAccession() - Method in class net.sourceforge.seqware.common.model.ShareLane
-
Getter for the field swAccession.
- getSwAccession() - Method in class net.sourceforge.seqware.common.model.ShareProcessing
-
Getter for the field swAccession.
- getSwAccession() - Method in class net.sourceforge.seqware.common.model.ShareSample
-
Getter for the field swAccession.
- getSwAccession() - Method in class net.sourceforge.seqware.common.model.ShareStudy
-
Getter for the field swAccession.
- getSwAccession() - Method in class net.sourceforge.seqware.common.model.ShareWorkflowRun
-
Getter for the field swAccession.
- getSwAccession() - Method in class net.sourceforge.seqware.common.model.Study
-
Getter for the field swAccession.
- getSwAccession() - Method in class net.sourceforge.seqware.common.model.Workflow
-
Getter for the field swAccession.
- getSwAccession() - Method in class net.sourceforge.seqware.common.model.WorkflowRun
-
Getter for the field swAccession.
- getSwCluster() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Environment
-
- getSyntax() - Static method in class net.sourceforge.seqware.pipeline.daxgenerator.Daxgenerator
-
getSyntax.
- getSyntax(OptionParser, String) - Static method in class net.sourceforge.seqware.pipeline.runner.Runner
-
getSyntax.
- getTag() - Method in class io.seqware.webservice.generated.model.ExpenseAttribute
-
- getTag() - Method in class io.seqware.webservice.generated.model.ExperimentAttribute
-
- getTag() - Method in class io.seqware.webservice.generated.model.FileAttribute
-
- getTag() - Method in class io.seqware.webservice.generated.model.InvoiceAttribute
-
- getTag() - Method in class io.seqware.webservice.generated.model.Ius
-
- getTag() - Method in class io.seqware.webservice.generated.model.IusAttribute
-
- getTag() - Method in class io.seqware.webservice.generated.model.LaneAttribute
-
- getTag() - Method in class io.seqware.webservice.generated.model.ProcessingAttribute
-
- getTag() - Method in class io.seqware.webservice.generated.model.SampleAttribute
-
- getTag() - Method in class io.seqware.webservice.generated.model.SampleSearchAttribute
-
- getTag() - Method in class io.seqware.webservice.generated.model.SequencerRunAttribute
-
- getTag() - Method in class io.seqware.webservice.generated.model.StudyAttribute
-
- getTag() - Method in class io.seqware.webservice.generated.model.WorkflowAttribute
-
- getTag() - Method in class io.seqware.webservice.generated.model.WorkflowRunAttribute
-
- getTag() - Method in interface net.sourceforge.seqware.common.model.Attribute
-
getTag.
- getTag() - Method in class net.sourceforge.seqware.common.model.ExperimentAttribute
-
Getter for the field tag.
- getTag() - Method in class net.sourceforge.seqware.common.model.FileAttribute
-
getTag.
- getTag() - Method in class net.sourceforge.seqware.common.model.IUS
-
Getter for the field tag.
- getTag() - Method in class net.sourceforge.seqware.common.model.IUSAttribute
-
getTag.
- getTag() - Method in class net.sourceforge.seqware.common.model.LaneAttribute
-
Getter for the field tag.
- getTag() - Method in class net.sourceforge.seqware.common.model.ProcessingAttribute
-
getTag.
- getTag() - Method in class net.sourceforge.seqware.common.model.SampleAttribute
-
getTag.
- getTag() - Method in class net.sourceforge.seqware.common.model.SampleSearchAttribute
-
getTag.
- getTag() - Method in class net.sourceforge.seqware.common.model.SequencerRunAttribute
-
Getter for the field tag.
- getTag() - Method in class net.sourceforge.seqware.common.model.StudyAttribute
-
getTag.
- getTag() - Method in class net.sourceforge.seqware.common.model.WorkflowAttribute
-
getTag.
- getTag() - Method in class net.sourceforge.seqware.common.model.WorkflowRunAttribute
-
getTag.
- getTag() - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.TagValueUnit
-
- getTagMetadata() - Method in class net.sourceforge.seqware.queryengine.webservice.model.MetadataDB
-
getTagMetadata.
- getTagMetadata(long) - Method in class net.sourceforge.seqware.queryengine.webservice.model.MetadataDB
-
getTagMetadata.
- getTags() - Method in class io.seqware.webservice.generated.model.Lane
-
- getTags() - Method in class io.seqware.webservice.generated.model.Sample
-
- getTags() - Method in class net.sourceforge.seqware.common.model.Lane
-
Getter for the field tags.
- getTags() - Method in class net.sourceforge.seqware.common.model.Sample
-
Getter for the field
tags.
- getTags() - Method in class net.sourceforge.seqware.pipeline.workflowV2.AbstractWorkflowDataModel
-
the key-value from metadata.xml
- getTagSpec() - Method in class io.seqware.webservice.generated.model.ExperimentSpotDesign
-
- getTagSpec() - Method in class net.sourceforge.seqware.common.model.ExperimentSpotDesign
-
Getter for the field tagSpec.
- getTargetedResequencing() - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.SampleInfo
-
Get the value of targetedResequencing
- getTaskGroup() - Method in class io.seqware.webservice.generated.model.Processing
-
- getTaxonId() - Method in class io.seqware.webservice.generated.model.Sample
-
- getTemplate() - Method in class net.sourceforge.seqware.common.model.Workflow
-
Getter for the field template.
- getTemplate() - Method in class net.sourceforge.seqware.common.model.WorkflowRun
-
Getter for the field template.
- getTemplateEmail() - Method in class net.sourceforge.seqware.common.invitation.InvitationParams
-
Getter for the field templateEmail.
- getTemplatePath() - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowInfo
-
Getter for the field templatePath.
- getTemplateType() - Method in class net.sourceforge.solexatools.webapp.metamodel.StudySampleReportFileLineItem
-
Getter for the field templateType.
- getTest() - Method in class net.sourceforge.seqware.pipeline.deciders.BasicDecider
-
- getTestCmd() - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowInfo
-
Getter for the field testCmd.
- getTests() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Workflow
-
- getThreads() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.AbstractJob
-
- getThreads() - Method in interface net.sourceforge.seqware.pipeline.workflowV2.model.Job
-
- getThreads() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.JobBatch
-
- getTimeTaken() - Method in class net.sourceforge.seqware.common.hibernate.reports.WorkflowRunReportRow
-
Getter for the field timeTaken.
- getTissSource() - Method in class net.sourceforge.solexatools.webapp.metamodel.StudySampleReportFileLineItem
-
Getter for the field tissSource.
- getTissueOrigin() - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.SampleInfo
-
Get the value of tissueOrigin
- getTissuePreparation() - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.SampleInfo
-
Get the value of tissuePreparation
- getTissueType() - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.SampleInfo
-
Get the value of tissueType
- getTitle() - Method in class io.seqware.webservice.generated.model.Experiment
-
- getTitle() - Method in class io.seqware.webservice.generated.model.Sample
-
- getTitle() - Method in class io.seqware.webservice.generated.model.Study
-
- getTitle() - Method in enum net.sourceforge.seqware.common.hibernate.FindAllTheFiles.Header
-
- getTitle() - Method in class net.sourceforge.seqware.common.model.Experiment
-
Getter for the field title.
- getTitle() - Method in class net.sourceforge.seqware.common.model.Sample
-
Getter for the field
title.
- getTitle() - Method in class net.sourceforge.seqware.common.model.Study
-
Getter for the field title.
- getTotal() - Method in class net.sourceforge.solexatools.webapp.metamodel.Flexigrid
-
Getter for the field total.
- getTotalPrice() - Method in class io.seqware.webservice.generated.model.Expense
-
- getTotalPrice() - Method in class net.sourceforge.seqware.common.model.Expense
-
Getter for the field
totalPrice.
- getTotalPriceString() - Method in class net.sourceforge.seqware.common.model.Expense
-
Getter for the field
totalPrice.
- getTotalUnits() - Method in class io.seqware.webservice.generated.model.Expense
-
- getTotalUnits() - Method in class net.sourceforge.seqware.common.model.Expense
-
Getter for the field
totalUnits.
- getType() - Method in class io.seqware.webservice.generated.model.File
-
- getType() - Method in class io.seqware.webservice.generated.model.Lane
-
- getType() - Method in class io.seqware.webservice.generated.model.Sample
-
- getType() - Method in class io.seqware.webservice.generated.model.WorkflowParam
-
- getType() - Method in class io.seqware.webservice.generated.model.WorkflowRunParam
-
- getType() - Method in class net.sourceforge.seqware.common.model.File
-
Getter for the field type.
- getType() - Method in class net.sourceforge.seqware.common.model.Sample
-
Getter for the field
type.
- getType() - Method in class net.sourceforge.seqware.common.model.UploadSequence
-
Getter for the field type.
- getType() - Method in class net.sourceforge.seqware.common.model.WorkflowParam
-
Getter for the field type.
- getType() - Method in class net.sourceforge.seqware.common.model.WorkflowRunParam
-
Getter for the field type.
- getType() - Method in class net.sourceforge.seqware.common.module.FileMetadata
-
- getType() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Requirement
-
- getType() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.SqwFile
-
- getType() - Method in class net.sourceforge.seqware.webservice.dto.FileDto
-
Getter for the field type.
- getType() - Method in class net.sourceforge.solexatools.webapp.controller.SearchController
-
Getter for the field type.
- getTypeNode() - Method in class net.sourceforge.seqware.common.business.UploadFile
-
Getter for the field typeNode.
- getUids(NamingEnumeration<SearchResult>) - Method in class net.sourceforge.solexatools.authentication.OICRLdapAuthentication
-
getUids.
- getUniqueDir() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.SqwFile
-
return the unqiue dir associate with the file
if the file type is input, the provisioned file will be output to provisionfiles/uniquedir + filename
- getUnit() - Method in class io.seqware.webservice.generated.model.FileAttribute
-
- getUnit() - Method in class io.seqware.webservice.generated.model.WorkflowAttribute
-
- getUnit() - Method in class io.seqware.webservice.generated.model.WorkflowRunAttribute
-
- getUnit() - Method in interface net.sourceforge.seqware.common.model.Attribute
-
getUnit.
- getUnit() - Method in class net.sourceforge.seqware.common.model.ExperimentAttribute
-
- getUnit() - Method in class net.sourceforge.seqware.common.model.FileAttribute
-
getUnit.
- getUnit() - Method in class net.sourceforge.seqware.common.model.IUSAttribute
-
getUnit.
- getUnit() - Method in class net.sourceforge.seqware.common.model.LaneAttribute
-
- getUnit() - Method in class net.sourceforge.seqware.common.model.ProcessingAttribute
-
getUnit.
- getUnit() - Method in class net.sourceforge.seqware.common.model.SampleAttribute
-
getUnit.
- getUnit() - Method in class net.sourceforge.seqware.common.model.SampleSearchAttribute
-
getUnit.
- getUnit() - Method in class net.sourceforge.seqware.common.model.SequencerRunAttribute
-
getUnit.
- getUnit() - Method in class net.sourceforge.seqware.common.model.StudyAttribute
-
getUnit.
- getUnit() - Method in class net.sourceforge.seqware.common.model.WorkflowAttribute
-
getUnit.
- getUnit() - Method in class net.sourceforge.seqware.common.model.WorkflowRunAttribute
-
getUnit.
- getUnit() - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.TagValueUnit
-
- getUnit() - Method in class net.sourceforge.seqware.webservice.dto.AttributeDto
-
Getter for the field unit.
- getUnits() - Method in class io.seqware.webservice.generated.model.ExpenseAttribute
-
- getUnits() - Method in class io.seqware.webservice.generated.model.ExperimentAttribute
-
- getUnits() - Method in class io.seqware.webservice.generated.model.InvoiceAttribute
-
- getUnits() - Method in class io.seqware.webservice.generated.model.IusAttribute
-
- getUnits() - Method in class io.seqware.webservice.generated.model.LaneAttribute
-
- getUnits() - Method in class io.seqware.webservice.generated.model.ProcessingAttribute
-
- getUnits() - Method in class io.seqware.webservice.generated.model.SampleAttribute
-
- getUnits() - Method in class io.seqware.webservice.generated.model.SequencerRunAttribute
-
- getUnits() - Method in class io.seqware.webservice.generated.model.StudyAttribute
-
- getUnits() - Method in class net.sourceforge.seqware.common.model.ExperimentAttribute
-
Getter for the field units.
- getUnits() - Method in class net.sourceforge.seqware.common.model.IUSAttribute
-
Getter for the field units.
- getUnits() - Method in class net.sourceforge.seqware.common.model.LaneAttribute
-
Getter for the field units.
- getUnits() - Method in class net.sourceforge.seqware.common.model.ProcessingAttribute
-
Getter for the field units.
- getUnits() - Method in class net.sourceforge.seqware.common.model.SampleAttribute
-
Getter for the field units.
- getUnits() - Method in class net.sourceforge.seqware.common.model.SequencerRunAttribute
-
Getter for the field units.
- getUnits() - Method in class net.sourceforge.seqware.common.model.StudyAttribute
-
Getter for the field units.
- getUpdateTimestamp() - Method in class net.sourceforge.seqware.common.model.Experiment
-
Getter for the field updateTimestamp.
- getUpdateTimestamp() - Method in class net.sourceforge.seqware.common.model.IUS
-
Getter for the field updateTimestamp.
- getUpdateTimestamp() - Method in class net.sourceforge.seqware.common.model.Lane
-
Getter for the field updateTimestamp.
- getUpdateTimestamp() - Method in class net.sourceforge.seqware.common.model.Processing
-
Getter for the field updateTimestamp.
- getUpdateTimestamp() - Method in class net.sourceforge.seqware.common.model.Registration
-
Getter for the field updateTimestamp.
- getUpdateTimestamp() - Method in class net.sourceforge.seqware.common.model.Sample
-
Getter for the field
updateTimestamp.
- getUpdateTimestamp() - Method in class net.sourceforge.seqware.common.model.SequencerRun
-
Getter for the field updateTimestamp.
- getUpdateTimestamp() - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
-
Getter for the field updateTimestamp.
- getUpdateTimestamp() - Method in class net.sourceforge.seqware.common.model.ShareStudy
-
Getter for the field updateTimestamp.
- getUpdateTimestamp() - Method in class net.sourceforge.seqware.common.model.ShareWorkflowRun
-
Getter for the field updateTimestamp.
- getUpdateTimestamp() - Method in class net.sourceforge.seqware.common.model.Study
-
Getter for the field updateTimestamp.
- getUpdateTimestamp() - Method in class net.sourceforge.seqware.common.model.Workflow
-
Getter for the field updateTimestamp.
- getUpdateTimestamp() - Method in class net.sourceforge.seqware.common.model.WorkflowRun
-
Getter for the field updateTimestamp.
- getUpdateTimeStamp() - Method in class net.sourceforge.seqware.webservice.dto.IusDto
-
Getter for the field updateTimeStamp.
- getUpdateTimeStamp() - Method in class net.sourceforge.seqware.webservice.dto.LibraryDto
-
Getter for the field updateTimeStamp.
- getUpdateTstmp() - Method in class io.seqware.webservice.generated.model.Experiment
-
- getUpdateTstmp() - Method in class io.seqware.webservice.generated.model.Ius
-
- getUpdateTstmp() - Method in class io.seqware.webservice.generated.model.Lane
-
- getUpdateTstmp() - Method in class io.seqware.webservice.generated.model.Processing
-
- getUpdateTstmp() - Method in class io.seqware.webservice.generated.model.Sample
-
- getUpdateTstmp() - Method in class io.seqware.webservice.generated.model.SequencerRun
-
- getUpdateTstmp() - Method in class io.seqware.webservice.generated.model.ShareExperiment
-
- getUpdateTstmp() - Method in class io.seqware.webservice.generated.model.ShareFile
-
- getUpdateTstmp() - Method in class io.seqware.webservice.generated.model.ShareLane
-
- getUpdateTstmp() - Method in class io.seqware.webservice.generated.model.ShareProcessing
-
- getUpdateTstmp() - Method in class io.seqware.webservice.generated.model.ShareSample
-
- getUpdateTstmp() - Method in class io.seqware.webservice.generated.model.ShareStudy
-
- getUpdateTstmp() - Method in class io.seqware.webservice.generated.model.ShareWorkflowRun
-
- getUpdateTstmp() - Method in class io.seqware.webservice.generated.model.Study
-
- getUpdateTstmp() - Method in class io.seqware.webservice.generated.model.Workflow
-
- getUpdateTstmp() - Method in class io.seqware.webservice.generated.model.WorkflowRun
-
- getUpdateTstmp() - Method in class net.sourceforge.seqware.common.model.ShareExperiment
-
Getter for the field updateTstmp.
- getUpdateTstmp() - Method in class net.sourceforge.seqware.common.model.ShareFile
-
Getter for the field updateTstmp.
- getUpdateTstmp() - Method in class net.sourceforge.seqware.common.model.ShareLane
-
Getter for the field updateTstmp.
- getUpdateTstmp() - Method in class net.sourceforge.seqware.common.model.ShareProcessing
-
Getter for the field updateTstmp.
- getUpdateTstmp() - Method in class net.sourceforge.seqware.common.model.ShareSample
-
Getter for the field updateTstmp.
- getUpdateValidator() - Method in class net.sourceforge.solexatools.webapp.controller.ExperimentController
-
Getter for the field updateValidator.
- getUpdateValidator() - Method in class net.sourceforge.solexatools.webapp.controller.StudyController
-
getUpdateValidator.
- getUrl() - Method in class io.seqware.webservice.generated.model.ExperimentLink
-
- getUrl() - Method in class io.seqware.webservice.generated.model.File
-
- getUrl() - Method in class io.seqware.webservice.generated.model.IusLink
-
- getUrl() - Method in class io.seqware.webservice.generated.model.LaneLink
-
- getUrl() - Method in class io.seqware.webservice.generated.model.Processing
-
- getUrl() - Method in class io.seqware.webservice.generated.model.ProcessingExperiments
-
- getUrl() - Method in class io.seqware.webservice.generated.model.ProcessingIus
-
- getUrl() - Method in class io.seqware.webservice.generated.model.ProcessingLanes
-
- getUrl() - Method in class io.seqware.webservice.generated.model.ProcessingSamples
-
- getUrl() - Method in class io.seqware.webservice.generated.model.ProcessingSequencerRuns
-
- getUrl() - Method in class io.seqware.webservice.generated.model.ProcessingStudies
-
- getUrl() - Method in class io.seqware.webservice.generated.model.SampleLink
-
- getUrl() - Method in class io.seqware.webservice.generated.model.StudyLink
-
- getUrl() - Method in class net.sourceforge.seqware.common.model.ExperimentLink
-
Getter for the field url.
- getUrl() - Method in class net.sourceforge.seqware.common.model.File
-
Getter for the field url.
- getUrl() - Method in class net.sourceforge.seqware.common.model.IUSLink
-
Getter for the field url.
- getUrl() - Method in class net.sourceforge.seqware.common.model.LaneLink
-
Getter for the field url.
- getUrl() - Method in class net.sourceforge.seqware.common.model.Processing
-
Getter for the field url.
- getUrl() - Method in class net.sourceforge.seqware.common.model.ProcessingExperiments
-
Getter for the field url.
- getUrl() - Method in class net.sourceforge.seqware.common.model.ProcessingIus
-
Getter for the field url.
- getUrl() - Method in class net.sourceforge.seqware.common.model.ProcessingLanes
-
Getter for the field url.
- getUrl() - Method in class net.sourceforge.seqware.common.model.ProcessingSamples
-
Getter for the field url.
- getUrl() - Method in class net.sourceforge.seqware.common.model.ProcessingSequencerRuns
-
Getter for the field url.
- getUrl() - Method in class net.sourceforge.seqware.common.model.ProcessingStudies
-
Getter for the field url.
- getUrl() - Method in class net.sourceforge.seqware.common.model.SampleLink
-
Getter for the field url.
- getUrl() - Method in class net.sourceforge.seqware.common.model.StudyLink
-
Getter for the field url.
- getUrl() - Method in class net.sourceforge.seqware.common.module.FileMetadata
-
- getUrl() - Method in class net.sourceforge.seqware.common.module.ReturnValue
-
Getter for the field url.
- getUrl() - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object.Pfn
-
Getter for the field url.
- getUrl() - Method in class net.sourceforge.seqware.webservice.dto.AttributeDto
-
Getter for the field url.
- getUrl() - Method in class net.sourceforge.seqware.webservice.dto.FileDto
-
Getter for the field url.
- getUrl() - Method in class net.sourceforge.seqware.webservice.dto.IusDto
-
Getter for the field url.
- getUrl() - Method in class net.sourceforge.seqware.webservice.dto.LibraryDto
-
Getter for the field url.
- getUrl() - Method in class net.sourceforge.seqware.webservice.dto.SampleSearchDto
-
Getter for the field url.
- getUrlLabel() - Method in class io.seqware.webservice.generated.model.File
-
- getUrlLabel() - Method in class io.seqware.webservice.generated.model.Processing
-
- getUrlLabel() - Method in class net.sourceforge.seqware.common.model.File
-
Getter for the field urlLabel.
- getUrlLabel() - Method in class net.sourceforge.seqware.common.model.Processing
-
Getter for the field urlLabel.
- getUrlLabel() - Method in class net.sourceforge.seqware.common.module.FileMetadata
-
- getUrlLabel() - Method in class net.sourceforge.seqware.common.module.ReturnValue
-
Getter for the field urlLabel.
- getUseIparIntensities() - Method in class io.seqware.webservice.generated.model.SequencerRun
-
- getUseIparIntensities() - Method in class net.sourceforge.seqware.common.model.SequencerRun
-
Getter for the field useIparIntensities.
- getUseIparIntensities() - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
-
Getter for the field useIparIntensities.
- getUseOneURL() - Method in class net.sourceforge.seqware.common.model.UploadSequence
-
Getter for the field useOneURL.
- getUserMl() - Method in class io.seqware.webservice.generated.model.Registration
-
- getUsername() - Method in class io.seqware.webservice.generated.model.Workflow
-
- getUsername() - Method in class io.seqware.webservice.generated.model.WorkflowRun
-
- getUsername() - Method in class net.sourceforge.seqware.common.model.Workflow
-
Getter for the field username.
- getUserName() - Method in class net.sourceforge.seqware.common.model.WorkflowRun
-
Getter for the field userName.
- getUseTwoURL() - Method in class net.sourceforge.seqware.common.model.UploadSequence
-
Getter for the field useTwoURL.
- getUseURL() - Method in class net.sourceforge.seqware.common.business.UploadFile
-
Getter for the field useURL.
- getValidationReportService() - Method in class net.sourceforge.seqware.common.ContextImpl
-
Getter for the field validationReportService.
- getValidator() - Method in class net.sourceforge.solexatools.webapp.controller.ExperimentController
-
Getter for the field validator.
- getValidator() - Method in class net.sourceforge.solexatools.webapp.controller.FileController
-
Getter for the field validator.
- getValidator() - Method in class net.sourceforge.solexatools.webapp.controller.LaneController
-
Getter for the field validator.
- getValidator() - Method in class net.sourceforge.solexatools.webapp.controller.ProcessingController
-
Getter for the field validator.
- getValidator() - Method in class net.sourceforge.solexatools.webapp.controller.RegistrationController
-
Getter for the field validator.
- getValidator() - Method in class net.sourceforge.solexatools.webapp.controller.SampleController
-
Getter for the field validator.
- getValidator() - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunController
-
Getter for the field validator.
- getValidator() - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunControllerDTO
-
Getter for the field validator.
- getValidator() - Method in class net.sourceforge.solexatools.webapp.controller.StudyController
-
getValidator.
- getValidator() - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileController
-
Getter for the field validator.
- getValidator() - Method in class net.sourceforge.solexatools.webapp.controller.UploadSequenceController
-
Getter for the field validator.
- getValidator() - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowController
-
Getter for the field validator.
- getValidator() - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowParamController
-
Getter for the field validator.
- getValidator() - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowParamValueController
-
Getter for the field validator.
- getValidator() - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowRunController
-
Getter for the field validator.
- getValue() - Method in class io.seqware.webservice.generated.model.ExpenseAttribute
-
- getValue() - Method in class io.seqware.webservice.generated.model.ExperimentAttribute
-
- getValue() - Method in class io.seqware.webservice.generated.model.FileAttribute
-
- getValue() - Method in class io.seqware.webservice.generated.model.InvoiceAttribute
-
- getValue() - Method in class io.seqware.webservice.generated.model.IusAttribute
-
- getValue() - Method in class io.seqware.webservice.generated.model.LaneAttribute
-
- getValue() - Method in class io.seqware.webservice.generated.model.ProcessingAttribute
-
- getValue() - Method in class io.seqware.webservice.generated.model.SampleAttribute
-
- getValue() - Method in class io.seqware.webservice.generated.model.SampleSearchAttribute
-
- getValue() - Method in class io.seqware.webservice.generated.model.SequencerRunAttribute
-
- getValue() - Method in class io.seqware.webservice.generated.model.StudyAttribute
-
- getValue() - Method in class io.seqware.webservice.generated.model.WorkflowAttribute
-
- getValue() - Method in class io.seqware.webservice.generated.model.WorkflowParamValue
-
- getValue() - Method in class io.seqware.webservice.generated.model.WorkflowRunAttribute
-
- getValue() - Method in class io.seqware.webservice.generated.model.WorkflowRunParam
-
- getValue() - Method in interface net.sourceforge.seqware.common.model.Attribute
-
getValue.
- getValue() - Method in class net.sourceforge.seqware.common.model.ExperimentAttribute
-
Getter for the field value.
- getValue() - Method in class net.sourceforge.seqware.common.model.FileAttribute
-
getValue.
- getValue() - Method in class net.sourceforge.seqware.common.model.IUSAttribute
-
getValue.
- getValue() - Method in class net.sourceforge.seqware.common.model.LaneAttribute
-
Getter for the field value.
- getValue() - Method in class net.sourceforge.seqware.common.model.ProcessingAttribute
-
getValue.
- getValue() - Method in class net.sourceforge.seqware.common.model.SampleAttribute
-
getValue.
- getValue() - Method in class net.sourceforge.seqware.common.model.SampleSearchAttribute
-
getValue.
- getValue() - Method in class net.sourceforge.seqware.common.model.SequencerRunAttribute
-
Getter for the field value.
- getValue() - Method in class net.sourceforge.seqware.common.model.StudyAttribute
-
getValue.
- getValue() - Method in class net.sourceforge.seqware.common.model.WorkflowAttribute
-
getValue.
- getValue() - Method in class net.sourceforge.seqware.common.model.WorkflowParam
-
Getter for the field value.
- getValue() - Method in class net.sourceforge.seqware.common.model.WorkflowParamValue
-
Getter for the field value.
- getValue() - Method in class net.sourceforge.seqware.common.model.WorkflowRunAttribute
-
getValue.
- getValue() - Method in class net.sourceforge.seqware.common.model.WorkflowRunParam
-
Getter for the field value.
- getValue() - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.TagValueUnit
-
- getValue() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Argument
-
Getter for the field value.
- getValue() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.JobProfile
-
Getter for the field value.
- getValue() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Requirement
-
- getValue() - Method in class net.sourceforge.seqware.webservice.dto.AttributeDto
-
Getter for the field value.
- getValues() - Method in class net.sourceforge.seqware.common.model.WorkflowParam
-
Getter for the field values.
- getVersion() - Method in class io.seqware.webservice.generated.model.Processing
-
- getVersion() - Method in class io.seqware.webservice.generated.model.Workflow
-
- getVersion() - Method in class net.sourceforge.seqware.common.model.Processing
-
Getter for the field version.
- getVersion() - Method in class net.sourceforge.seqware.common.model.Workflow
-
Getter for the field version.
- getVersion() - Method in class net.sourceforge.seqware.common.module.ReturnValue
-
Getter for the field version.
- getVersion() - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowInfo
-
Getter for the field version.
- getVersion() - Method in class net.sourceforge.seqware.pipeline.workflowV2.AbstractWorkflowDataModel
-
- getVersion() - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object.WorkflowExecutable
-
- getViaAccessions(int[]) - Method in interface net.sourceforge.seqware.common.metadata.Metadata
-
Get the models corresponding to potential accessions
- getViaAccessions(int[]) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
-
- getViaAccessions(int[]) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection
-
- getViaAccessions(int[]) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS
-
- getViaParentAccessions(int[]) - Method in interface net.sourceforge.seqware.common.metadata.Metadata
-
Get the models corresponding to potential parent accessions
- getViaParentAccessions(int[]) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
-
- getViaParentAccessions(int[]) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection
-
- getViaParentAccessions(int[]) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS
-
- getViewName(String) - Static method in class net.sourceforge.solexatools.util.Constant
-
getViewName.
- getVisibleParams() - Method in class net.sourceforge.solexatools.util.SummaryData
-
Getter for the field visibleParams.
- getVisibleWorkflowParams() - Method in class net.sourceforge.seqware.common.model.Workflow
-
getVisibleWorkflowParams.
- getVisibleWorkflowParamsWithDifferentValue() - Method in class net.sourceforge.seqware.common.model.Workflow
-
getVisibleWorkflowParamsWithDifferentValue.
- getWebResource() - Method in class io.seqware.webservice.generated.client.SeqWareWebserviceClient
-
- getWfRuns() - Method in class net.sourceforge.solexatools.webapp.metamodel.StudySampleReportLineItem
-
Getter for the field wfRuns.
- getWidth() - Method in class net.sourceforge.solexatools.webapp.metamodel.Flexigrid.ColumnModel
-
- getWorkflow(int) - Method in interface net.sourceforge.seqware.common.metadata.Metadata
-
Get a workflow
- getWorkflow(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
-
- getWorkflow(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection
-
- getWorkflow(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS
-
Get a workflow
- getWorkflow() - Method in class net.sourceforge.seqware.common.model.SampleReportRow
-
Getter for the field workflow.
- getWorkflow() - Method in class net.sourceforge.seqware.common.model.WorkflowAttribute
-
Getter for the field workflow.
- getWorkflow() - Method in class net.sourceforge.seqware.common.model.WorkflowParam
-
Getter for the field workflow.
- getWorkflow() - Method in class net.sourceforge.seqware.common.model.WorkflowRun
-
Getter for the field workflow.
- getWorkflow() - Method in class net.sourceforge.seqware.pipeline.workflowV2.AbstractWorkflowDataModel
-
- getWorkflow_accession() - Method in class net.sourceforge.seqware.pipeline.workflowV2.AbstractWorkflowDataModel
-
- getWorkflow_directory_name() - Method in class net.sourceforge.seqware.pipeline.workflowV2.AbstractWorkflowDataModel
-
- getWorkflow_engine() - Method in class net.sourceforge.seqware.pipeline.workflowV2.AbstractWorkflowDataModel
-
- getWorkflow_run_accession() - Method in class net.sourceforge.seqware.pipeline.workflowV2.AbstractWorkflowDataModel
-
- getWorkflowAccession(String, String) - Method in interface net.sourceforge.seqware.common.metadata.Metadata
-
getWorkflowAccession.
- getWorkflowAccession(String, String) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
-
getWorkflowAccession.
- getWorkflowAccession(String, String) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection
-
getWorkflowAccession.
- getWorkflowAccession(String, String) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS
-
getWorkflowAccession.
- getWorkflowAccession() - Method in class net.sourceforge.seqware.common.model.WorkflowRun
-
- getWorkflowAccession() - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowInfo
-
Getter for the field workflowAccession.
- getWorkflowAccession() - Method in class net.sourceforge.seqware.pipeline.deciders.BasicDecider
-
- getWorkflowAccession(int) - Method in class net.sourceforge.seqware.queryengine.webservice.model.MetadataDB
-
getWorkflowAccession.
- getWorkflowAccessionsToCheck() - Method in class net.sourceforge.seqware.pipeline.deciders.BasicDecider
-
- getWorkflowAttributeCollection() - Method in class io.seqware.webservice.generated.model.Workflow
-
- getWorkflowAttributeId() - Method in class io.seqware.webservice.generated.model.WorkflowAttribute
-
- getWorkflowAttributeId() - Method in class net.sourceforge.seqware.common.model.WorkflowAttribute
-
Getter for the field workflowAttributeId.
- getWorkflowAttributes() - Method in class net.sourceforge.seqware.common.model.Workflow
-
Getter for the field workflowAttributes.
- getWorkflowBaseDir() - Method in class net.sourceforge.seqware.pipeline.workflowV2.AbstractWorkflowDataModel
-
- getWorkflowBundleDir() - Method in class net.sourceforge.seqware.pipeline.workflowV2.AbstractWorkflowDataModel
-
- getWorkflowBundleDir() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Workflow
-
- getWorkflowClass() - Method in class io.seqware.webservice.generated.model.Workflow
-
- getWorkflowClass() - Method in class net.sourceforge.seqware.common.model.Workflow
-
- getWorkflowClass() - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowInfo
-
- getWorkflowCollection() - Method in class io.seqware.webservice.generated.model.Registration
-
- getWorkflowDataModel(Integer, Integer) - Method in class net.sourceforge.seqware.pipeline.workflowV2.WorkflowDataModelFactory
-
load metadata.xml, if FTL, parse the FTL to XML, and translate it to Java
based Object if Java, load the class.
- getWorkflowDir() - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowInfo
-
Getter for the field workflowDir.
- getWorkflowEngine() - Method in class io.seqware.webservice.generated.model.Workflow
-
- getWorkflowEngine() - Method in class io.seqware.webservice.generated.model.WorkflowRun
-
- getWorkflowEngine() - Method in class net.sourceforge.seqware.common.model.Workflow
-
- getWorkflowEngine() - Method in class net.sourceforge.seqware.common.model.WorkflowRun
-
- getWorkflowEngine() - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowInfo
-
- getWorkflowEngine(AbstractWorkflowDataModel, Map<String, String>) - Static method in class net.sourceforge.seqware.pipeline.plugin.WorkflowPlugin
-
- getWorkflowId() - Method in class io.seqware.webservice.generated.model.SampleReport
-
- getWorkflowId() - Method in class io.seqware.webservice.generated.model.Workflow
-
- getWorkflowId() - Method in class io.seqware.webservice.generated.model.WorkflowAttribute
-
- getWorkflowId() - Method in class io.seqware.webservice.generated.model.WorkflowParam
-
- getWorkflowId() - Method in class io.seqware.webservice.generated.model.WorkflowRun
-
- getWorkflowId() - Method in class net.sourceforge.seqware.common.model.Workflow
-
Getter for the field workflowId.
- getWorkflowInfo() - Method in class net.sourceforge.seqware.pipeline.bundle.BundleInfo
-
getWorkflowInfo.
- getWorkflowMetadata() - Method in class net.sourceforge.seqware.queryengine.webservice.model.MetadataDB
-
getWorkflowMetadata.
- getWorkflowParam() - Method in class net.sourceforge.seqware.common.model.WorkflowParamValue
-
Getter for the field workflowParam.
- getWorkflowParamCollection() - Method in class io.seqware.webservice.generated.model.Workflow
-
- getWorkflowParamId() - Method in class io.seqware.webservice.generated.model.WorkflowParam
-
- getWorkflowParamId() - Method in class io.seqware.webservice.generated.model.WorkflowParamValue
-
- getWorkflowParamId() - Method in class net.sourceforge.seqware.common.model.WorkflowParam
-
Getter for the field workflowParamId.
- getWorkflowParamId() - Method in class net.sourceforge.seqware.common.model.WorkflowParamValue
-
Getter for the field workflowParamId.
- getWorkflowParamMetadata(Integer) - Method in class net.sourceforge.seqware.queryengine.webservice.model.MetadataDB
-
getWorkflowParamMetadata.
- getWorkflowParams(String) - Method in interface net.sourceforge.seqware.common.metadata.Metadata
-
getWorkflowParams.
- getWorkflowParams(String) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
-
getWorkflowParams.
- getWorkflowParams(String) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection
-
getWorkflowParams.
- getWorkflowParams(String) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS
-
getWorkflowParams.
- getWorkflowParams() - Method in class net.sourceforge.seqware.common.model.Workflow
-
Getter for the field workflowParams.
- getWorkflowParamService() - Method in class net.sourceforge.seqware.common.ContextImpl
-
Getter for the field workflowParamService.
- getWorkflowParamService() - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowParamController
-
Getter for the field workflowParamService.
- getWorkflowParamService() - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowParamSetupController
-
Getter for the field workflowParamService.
- getWorkflowParamService() - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowParamValueSetupController
-
Getter for the field workflowParamService.
- getWorkflowParamServiceBean() - Static method in class net.sourceforge.seqware.common.factory.BeanFactory
-
getWorkflowParamServiceBean.
- getWorkflowParamsWithDifferentFileMetaType() - Method in class net.sourceforge.seqware.common.model.Workflow
-
getWorkflowParamsWithDifferentFileMetaType.
- getWorkflowParamValueCollection() - Method in class io.seqware.webservice.generated.model.WorkflowParam
-
- getWorkflowParamValueId() - Method in class io.seqware.webservice.generated.model.WorkflowParamValue
-
- getWorkflowParamValueId() - Method in class net.sourceforge.seqware.common.model.WorkflowParamValue
-
Getter for the field workflowParamValueId.
- getWorkflowParamValueService() - Method in class net.sourceforge.seqware.common.ContextImpl
-
Getter for the field workflowParamValueService.
- getWorkflowParamValueService() - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowParamValueController
-
Getter for the field workflowParamValueService.
- getWorkflowParamValueService() - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowParamValueSetupController
-
Getter for the field workflowParamValueService.
- getWorkflowParamValueServiceBean() - Static method in class net.sourceforge.seqware.common.factory.BeanFactory
-
getWorkflowParamValueServiceBean.
- getWorkflowRun() - Method in class net.sourceforge.seqware.common.hibernate.reports.WorkflowRunReportRow
-
Getter for the field workflowRun.
- getWorkflowRun(int) - Method in interface net.sourceforge.seqware.common.metadata.Metadata
-
getWorkflowRun.
- getWorkflowRun(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
-
getWorkflowRun.
- getWorkflowRun(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection
-
getWorkflowRun.
- getWorkflowRun(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS
-
getWorkflowRun.
- getWorkflowRun() - Method in class net.sourceforge.seqware.common.model.Expense
-
Getter for the field
workflowRun.
- getWorkflowRun() - Method in class net.sourceforge.seqware.common.model.Processing
-
Getter for the field workflowRun.
- getWorkflowRun() - Method in class net.sourceforge.seqware.common.model.WorkflowRunAttribute
-
Getter for the field workflowRun.
- getWorkflowRun() - Method in class net.sourceforge.seqware.common.model.WorkflowRunParam
-
Getter for the field workflowRun.
- getWorkflowRunAccession() - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object.OozieJob
-
- getWorkflowRunAccession() - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object.PegasusJob
-
- getWorkflowRunAttributeCollection() - Method in class io.seqware.webservice.generated.model.WorkflowRun
-
- getWorkflowRunAttributeId() - Method in class io.seqware.webservice.generated.model.WorkflowRunAttribute
-
- getWorkflowRunAttributeId() - Method in class net.sourceforge.seqware.common.model.WorkflowRunAttribute
-
Getter for the field workflowRunAttributeId.
- getWorkflowRunAttributes() - Method in class net.sourceforge.seqware.common.model.WorkflowRun
-
Getter for the field workflowRunAttributes.
- getWorkflowRunByAncestorWorkflowRunId() - Method in class net.sourceforge.seqware.common.model.Processing
-
Getter for the field workflowRunByAncestorWorkflowRunId.
- getWorkflowRunCollection() - Method in class io.seqware.webservice.generated.model.File
-
- getWorkflowRunCollection() - Method in class io.seqware.webservice.generated.model.Registration
-
- getWorkflowRunCollection() - Method in class io.seqware.webservice.generated.model.Workflow
-
- getWorkflowRunHtml(WorkflowRun, Registration, String, String, String) - Static method in class net.sourceforge.solexatools.util.NodeHtmlUtil
-
getWorkflowRunHtml.
- getWorkflowRunHtmlWithIUSs(WorkflowRun, Registration, String, String, String) - Static method in class net.sourceforge.solexatools.util.NodeHtmlUtil
-
getWorkflowRunHtmlWithIUSs.
- getWorkflowRunId() - Method in class io.seqware.webservice.generated.model.Expense
-
- getWorkflowRunId() - Method in class io.seqware.webservice.generated.model.IusWorkflowRuns
-
- getWorkflowRunId() - Method in class io.seqware.webservice.generated.model.LaneWorkflowRuns
-
- getWorkflowRunId() - Method in class io.seqware.webservice.generated.model.Processing
-
- getWorkflowRunId() - Method in class io.seqware.webservice.generated.model.ShareWorkflowRun
-
- getWorkflowRunId() - Method in class io.seqware.webservice.generated.model.WorkflowRun
-
- getWorkflowRunId() - Method in class io.seqware.webservice.generated.model.WorkflowRunAttribute
-
- getWorkflowRunId() - Method in class io.seqware.webservice.generated.model.WorkflowRunParam
-
- getWorkflowRunId() - Method in class net.sourceforge.seqware.common.model.Processing
-
Getter for the field workflowRunId.
- getWorkflowRunId() - Method in class net.sourceforge.seqware.common.model.ShareWorkflowRun
-
Getter for the field workflowRunId.
- getWorkflowRunId() - Method in class net.sourceforge.seqware.common.model.WorkflowRun
-
Getter for the field workflowRunId.
- getWorkflowRunInfo(int) - Method in class net.sourceforge.seqware.queryengine.webservice.model.MetadataDB
-
getWorkflowRunInfo.
- getWorkflowRunParam(SortedSet<WorkflowParam>) - Static method in class net.sourceforge.solexatools.util.LaunchWorkflowUtil
-
getWorkflowRunParam.
- getWorkflowRunParamCollection() - Method in class io.seqware.webservice.generated.model.WorkflowRun
-
- getWorkflowRunParamId() - Method in class io.seqware.webservice.generated.model.WorkflowRunParam
-
- getWorkflowRunParamId() - Method in class net.sourceforge.seqware.common.model.WorkflowRunParam
-
getWorkflowRunParamId.
- getWorkflowRunParams() - Method in class net.sourceforge.seqware.common.model.WorkflowRun
-
Getter for the field workflowRunParams.
- getWorkflowRunProcessings() - Method in class net.sourceforge.seqware.common.hibernate.reports.WorkflowRunReportRow
-
Getter for the field workflowRunProcessings.
- getWorkflowRunReport(int) - Method in interface net.sourceforge.seqware.common.metadata.Metadata
-
getWorkflowRunReport.
- getWorkflowRunReport(int, Date, Date) - Method in interface net.sourceforge.seqware.common.metadata.Metadata
-
getWorkflowRunReport.
- getWorkflowRunReport(Date, Date) - Method in interface net.sourceforge.seqware.common.metadata.Metadata
-
getWorkflowRunReport.
- getWorkflowRunReport(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
-
getWorkflowRunReport.
- getWorkflowRunReport(int, Date, Date) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
-
getWorkflowRunReport.
- getWorkflowRunReport(Date, Date) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
-
getWorkflowRunReport.
- getWorkflowRunReport(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection
-
getWorkflowRunReport.
- getWorkflowRunReport(int, Date, Date) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection
-
getWorkflowRunReport.
- getWorkflowRunReport(Date, Date) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection
-
getWorkflowRunReport.
- getWorkflowRunReport(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS
-
getWorkflowRunReport.
- getWorkflowRunReport(int, Date, Date) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS
-
getWorkflowRunReport.
- getWorkflowRunReport(Date, Date) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS
-
getWorkflowRunReport.
- getWorkflowRunReportStdErr(int) - Method in interface net.sourceforge.seqware.common.metadata.Metadata
-
getWorkflowRunReportStdErr.
- getWorkflowRunReportStdErr(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
-
- getWorkflowRunReportStdErr(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection
-
- getWorkflowRunReportStdErr(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS
-
getWorkflowRunReportStdErr.
- getWorkflowRunReportStdOut(int) - Method in interface net.sourceforge.seqware.common.metadata.Metadata
-
getWorkflowRunReportStdOut.
- getWorkflowRunReportStdOut(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
-
- getWorkflowRunReportStdOut(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection
-
- getWorkflowRunReportStdOut(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS
-
getWorkflowRunReportStdOut.
- getWorkflowRuns() - Method in class net.sourceforge.seqware.common.model.IUS
-
Getter for the field workflowRuns.
- getWorkflowRuns() - Method in class net.sourceforge.seqware.common.model.Lane
-
Getter for the field workflowRuns.
- getWorkflowRuns() - Method in class net.sourceforge.seqware.common.model.Workflow
-
Getter for the field workflowRuns.
- getWorkflowRunsAssociatedWithFiles(List<Integer>, String) - Method in interface net.sourceforge.seqware.common.metadata.Metadata
-
Returns the workflow_runs associated with a group of files.
- getWorkflowRunsAssociatedWithFiles(List<Integer>, String) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
-
- getWorkflowRunsAssociatedWithFiles(List<Integer>, String) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection
-
- getWorkflowRunsAssociatedWithFiles(List<Integer>, String) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS
-
- getWorkflowRunsAssociatedWithInputFiles(List<Integer>) - Method in interface net.sourceforge.seqware.common.metadata.Metadata
-
Returns the workflow_runs associated with a group of input files.
- getWorkflowRunsAssociatedWithInputFiles(List<Integer>, List<Integer>) - Method in interface net.sourceforge.seqware.common.metadata.Metadata
-
Returns the workflow_runs associated with a group of input files.
- getWorkflowRunsAssociatedWithInputFiles(List<Integer>) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
-
- getWorkflowRunsAssociatedWithInputFiles(List<Integer>, List<Integer>) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
-
- getWorkflowRunsAssociatedWithInputFiles(List<Integer>) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection
-
- getWorkflowRunsAssociatedWithInputFiles(List<Integer>, List<Integer>) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection
-
- getWorkflowRunsAssociatedWithInputFiles(List<Integer>) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS
-
- getWorkflowRunsAssociatedWithInputFiles(List<Integer>, List<Integer>) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS
-
- getWorkflowRunsByHost(String) - Method in interface net.sourceforge.seqware.common.metadata.Metadata
-
getWorkflowRunsByHost.
- getWorkflowRunsByHost(String) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
-
getWorkflowRunsByHost.
- getWorkflowRunsByHost(String) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection
-
getWorkflowRunsByHost.
- getWorkflowRunsByHost(String) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS
-
getWorkflowRunsByHost.
- getWorkflowRunsByStatus(WorkflowRunStatus) - Method in interface net.sourceforge.seqware.common.metadata.Metadata
-
getWorkflowRunsByStatus.
- getWorkflowRunsByStatus(WorkflowRunStatus) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
-
getWorkflowRunsByStatus.
- getWorkflowRunsByStatus(WorkflowRunStatus) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection
-
getWorkflowRunsByStatus.
- getWorkflowRunsByStatus(WorkflowRunStatus) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS
-
getWorkflowRunsByStatus.
- getWorkflowRunService() - Method in class net.sourceforge.seqware.common.ContextImpl
-
Getter for the field workflowRunService.
- getWorkflowRunService() - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysBulkDownloadListController
-
Getter for the field workflowRunService.
- getWorkflowRunService() - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysBulkDownloadListDetailsController
-
Getter for the field workflowRunService.
- getWorkflowRunService() - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysEventController
-
Getter for the field workflowRunService.
- getWorkflowRunService() - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysListController
-
Getter for the field workflowRunService.
- getWorkflowRunService() - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysListDetailsController
-
Getter for the field workflowRunService.
- getWorkflowRunService() - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysRunningListDetailsController
-
Getter for the field workflowRunService.
- getWorkflowRunService() - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysTableController
-
Getter for the field
workflowRunService.
- getWorkflowRunService() - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysTableControllerDetails
-
Getter for the field
workflowRunService.
- getWorkflowRunService() - Method in class net.sourceforge.solexatools.webapp.controller.CancelAnalysisWorkflowController
-
Getter for the field workflowRunService.
- getWorkflowRunService() - Method in class net.sourceforge.solexatools.webapp.controller.DownloadFileListController
-
Getter for the field workflowRunService.
- getWorkflowRunService() - Method in class net.sourceforge.solexatools.webapp.controller.LaunchWorkflowController
-
Getter for the field workflowRunService.
- getWorkflowRunService() - Method in class net.sourceforge.solexatools.webapp.controller.RetryAnalysisWorkflowController
-
Getter for the field workflowRunService.
- getWorkflowRunService() - Method in class net.sourceforge.solexatools.webapp.controller.SelectInputController
-
Getter for the field workflowRunService.
- getWorkflowRunService() - Method in class net.sourceforge.solexatools.webapp.controller.SelectInputListController
-
Getter for the field workflowRunService.
- getWorkflowRunService() - Method in class net.sourceforge.solexatools.webapp.controller.ShareValidatorController
-
Getter for the field workflowRunService.
- getWorkflowRunService() - Method in class net.sourceforge.solexatools.webapp.controller.StudyListDetailsFlatController
-
Getter for the field workflowRunService.
- getWorkflowRunService() - Method in class net.sourceforge.solexatools.webapp.controller.SummaryLaunchWorkflowController
-
Getter for the field workflowRunService.
- getWorkflowRunService() - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowRunSetupController
-
Getter for the field workflowRunService.
- getWorkflowRunServiceBean() - Static method in class net.sourceforge.seqware.common.factory.BeanFactory
-
getWorkflowRunServiceBean.
- getWorkflowRunWithWorkflow(String) - Method in interface net.sourceforge.seqware.common.metadata.Metadata
-
getWorkflowRunWithWorkflow.
- getWorkflowRunWithWorkflow(String) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
-
getWorkflowRunWithWorkflow.
- getWorkflowRunWithWorkflow(String) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection
-
getWorkflowRunWithWorkflow.
- getWorkflowRunWithWorkflow(String) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS
-
getWorkflowRunWithWorkflow.
- getWorkflows(SequencerRun) - Method in class net.sourceforge.seqware.common.business.impl.SampleReportServiceImpl
-
getWorkflows.
- getWorkflows(SequencerRun) - Method in interface net.sourceforge.seqware.common.business.SampleReportService
-
getWorkflows.
- getWorkflows(SequencerRun) - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleReportDAOHibernate
-
getWorkflows.
- getWorkflows(SequencerRun) - Method in interface net.sourceforge.seqware.common.dao.SampleReportDAO
-
getWorkflows.
- getWorkflowsAndRuns() - Method in class net.sourceforge.seqware.common.hibernate.SequencerRunReport.Row
-
- getWorkflowService() - Method in class net.sourceforge.seqware.common.ContextImpl
-
Getter for the field workflowService.
- getWorkflowService() - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysListController
-
Getter for the field workflowService.
- getWorkflowService() - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysTableController
-
Getter for the field
workflowService.
- getWorkflowService() - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysTableControllerDetails
-
Getter for the field
workflowService.
- getWorkflowService() - Method in class net.sourceforge.solexatools.webapp.controller.ChangeWorkflowParamValueController
-
Getter for the field workflowService.
- getWorkflowService() - Method in class net.sourceforge.solexatools.webapp.controller.LaunchWorkflowController
-
Getter for the field workflowService.
- getWorkflowService() - Method in class net.sourceforge.solexatools.webapp.controller.LaunchWorkflowSetupController
-
Getter for the field workflowService.
- getWorkflowService() - Method in class net.sourceforge.solexatools.webapp.controller.ManageWorkflowsController
-
Getter for the field workflowService.
- getWorkflowService() - Method in class net.sourceforge.solexatools.webapp.controller.SelectInputController
-
Getter for the field workflowService.
- getWorkflowService() - Method in class net.sourceforge.solexatools.webapp.controller.SummaryLaunchWorkflowController
-
Getter for the field workflowService.
- getWorkflowService() - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowController
-
Getter for the field workflowService.
- getWorkflowService() - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowListSetupController
-
Getter for the field workflowService.
- getWorkflowService() - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowParamListController
-
Getter for the field workflowService.
- getWorkflowService() - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowSetupController
-
Getter for the field workflowService.
- getWorkflowServiceBean() - Static method in class net.sourceforge.seqware.common.factory.BeanFactory
-
getWorkflowServiceBean.
- getWorkflowsForStudy(Study) - Method in class net.sourceforge.seqware.common.business.impl.SampleReportServiceImpl
-
getWorkflowsForStudy.
- getWorkflowsForStudy(Study) - Method in interface net.sourceforge.seqware.common.business.SampleReportService
-
getWorkflowsForStudy.
- getWorkflowsForStudy(Study) - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleReportDAOHibernate
-
getWorkflowsForStudy.
- getWorkflowsForStudy(Study) - Method in interface net.sourceforge.seqware.common.dao.SampleReportDAO
-
getWorkflowsForStudy.
- getWorkflowSqwVersion() - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowInfo
-
getWorkflowSqwVersion.
- getWorkflowsRun() - Method in class net.sourceforge.solexatools.webapp.metamodel.SampleDetailsWorkflowLineItems
-
getWorkflowsRun.
- getWorkflowState(String) - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowTools
-
This method examines a Pegasus log directory using the status command
provided and will encode the state of the workflow in the ReturnValue
object, running as ReturnValue.PROCESSING, failed as ReturnValue.FAILURE,
and success as ReturnValue.SUCCESS.
- getWorkflowTemplate() - Method in class io.seqware.webservice.generated.model.Workflow
-
- getWorkflowTemplate() - Method in class io.seqware.webservice.generated.model.WorkflowRun
-
- getWorkflowType() - Method in class io.seqware.webservice.generated.model.Workflow
-
- getWorkflowType() - Method in class net.sourceforge.seqware.common.model.Workflow
-
- getWorkflowType() - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowInfo
-
- getWorkflowType() - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.RunInfo
-
Get the value of workflowType
- getWorkingDirectory() - Method in class net.sourceforge.seqware.pipeline.workflowV2.AbstractWorkflowEngine
-
The working directory for the prepared workflow run, or null if not yet
prepared or if not applicable for the concrete engine.
- getWorkingDirectory() - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.OozieWorkflowEngine
-
- getWorkingDirectory() - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.PegasusWorkflowEngine
-
- getWS(Map<String, String>) - Static method in class net.sourceforge.seqware.common.metadata.MetadataFactory
-
- getXml() - Method in class net.sourceforge.seqware.webservice.resources.filters.ExperimentIDFilter
-
getXml.
- getXml() - Method in class net.sourceforge.seqware.webservice.resources.filters.IUSIDFilter
-
getXml.
- getXml() - Method in class net.sourceforge.seqware.webservice.resources.filters.LaneIDFilter
-
getXml.
- getXml() - Method in class net.sourceforge.seqware.webservice.resources.filters.SampleIDFilter
-
getXml.
- getXml() - Method in class net.sourceforge.seqware.webservice.resources.tables.ExperimentIDResource
-
getXml.
- getXml() - Method in class net.sourceforge.seqware.webservice.resources.tables.ExperimentLibraryDesignResource
-
getXml.
- getXml() - Method in class net.sourceforge.seqware.webservice.resources.tables.ExperimentResource
-
getXml.
- getXml() - Method in class net.sourceforge.seqware.webservice.resources.tables.ExperimentSpotDesignReadSpecResource
-
getXml.
- getXml() - Method in class net.sourceforge.seqware.webservice.resources.tables.ExperimentSpotDesignResource
-
getXml.
- getXml() - Method in class net.sourceforge.seqware.webservice.resources.tables.FileChildWorkflowRunsResource
-
getXml.
- getXml() - Method in class net.sourceforge.seqware.webservice.resources.tables.FileIDResource
-
getXml.
- getXml() - Method in class net.sourceforge.seqware.webservice.resources.tables.FileResource
-
getXml.
- getXml() - Method in class net.sourceforge.seqware.webservice.resources.tables.IusIDResource
-
getXml.
- getXml() - Method in class net.sourceforge.seqware.webservice.resources.tables.IusResource
-
getXml.
- getXml() - Method in class net.sourceforge.seqware.webservice.resources.tables.LaneIDResource
-
getXml.
- getXml() - Method in class net.sourceforge.seqware.webservice.resources.tables.LaneResource
-
getXml.
- getXml() - Method in class net.sourceforge.seqware.webservice.resources.tables.LibrarySelectionResource
-
getXml.
- getXml() - Method in class net.sourceforge.seqware.webservice.resources.tables.LibrarySourceResource
-
getXml.
- getXml() - Method in class net.sourceforge.seqware.webservice.resources.tables.LibraryStrategyResource
-
getXml.
- getXml() - Method in class net.sourceforge.seqware.webservice.resources.tables.OrganismResource
-
getXml.
- getXml() - Method in class net.sourceforge.seqware.webservice.resources.tables.PlatformResource
-
getXml.
- getXml() - Method in class net.sourceforge.seqware.webservice.resources.tables.ProcessIDResource
-
getXml.
- getXml() - Method in class net.sourceforge.seqware.webservice.resources.tables.ProcessResource
-
getXml.
- getXml() - Method in class net.sourceforge.seqware.webservice.resources.tables.RootSampleResource
-
getXml.
- getXml() - Method in class net.sourceforge.seqware.webservice.resources.tables.SampleIDResource
-
getXml.
- getXml() - Method in class net.sourceforge.seqware.webservice.resources.tables.SampleResource
-
getXml.
- getXml() - Method in class net.sourceforge.seqware.webservice.resources.tables.SequencerRunIDResource
-
getXml.
- getXml() - Method in class net.sourceforge.seqware.webservice.resources.tables.SequencerRunResource
-
getXml.
- getXml() - Method in class net.sourceforge.seqware.webservice.resources.tables.StudyIDResource
-
getXml.
- getXML() - Method in class net.sourceforge.seqware.webservice.resources.tables.StudyResource
-
getXML.
- getXml() - Method in class net.sourceforge.seqware.webservice.resources.tables.StudyTypeResource
-
getXml.
- getXml() - Method in class net.sourceforge.seqware.webservice.resources.tables.WorkflowIDResource
-
getXml.
- getXml() - Method in class net.sourceforge.seqware.webservice.resources.tables.WorkflowParamResource
-
getXml.
- getXml() - Method in class net.sourceforge.seqware.webservice.resources.tables.WorkflowParamValueResource
-
getXml.
- getXml() - Method in class net.sourceforge.seqware.webservice.resources.tables.WorkflowResource
-
getXml.
- getXml() - Method in class net.sourceforge.seqware.webservice.resources.tables.WorkflowRunIDResource
-
getXml.
- getXml() - Method in class net.sourceforge.seqware.webservice.resources.tables.WorkflowRunResource
-
getXml.
- givesPermission(Registration) - Method in class net.sourceforge.seqware.common.security.PermissionsAware
-
- givesPermission(Registration, Set<Integer>) - Method in class net.sourceforge.seqware.common.security.PermissionsAware
-
- givesPermissionInternal(Registration, Set<Integer>) - Method in class net.sourceforge.seqware.common.model.Expense
-
Short-circuit permission checking by providing a set of entities that have already been checked
- givesPermissionInternal(Registration, Set<Integer>) - Method in class net.sourceforge.seqware.common.model.Experiment
-
- givesPermissionInternal(Registration, Set<Integer>) - Method in class net.sourceforge.seqware.common.model.File
-
- givesPermissionInternal(Registration, Set<Integer>) - Method in class net.sourceforge.seqware.common.model.Invoice
-
- givesPermissionInternal(Registration, Set<Integer>) - Method in class net.sourceforge.seqware.common.model.IUS
-
- givesPermissionInternal(Registration, Set<Integer>) - Method in class net.sourceforge.seqware.common.model.Lane
-
- givesPermissionInternal(Registration, Set<Integer>) - Method in class net.sourceforge.seqware.common.model.Processing
-
Short-circuit permission checking by providing a set of entities that have already been checked
- givesPermissionInternal(Registration, Set<Integer>) - Method in class net.sourceforge.seqware.common.model.Registration
-
Short-circuit permission checking by providing a set of entities that have already been checked
- givesPermissionInternal(Registration, Set<Integer>) - Method in class net.sourceforge.seqware.common.model.Sample
-
Short-circuit permission checking by providing a set of entities that have already been checked
- givesPermissionInternal(Registration, Set<Integer>) - Method in class net.sourceforge.seqware.common.model.SequencerRun
-
Short-circuit permission checking by providing a set of entities that have already been checked
- givesPermissionInternal(Registration, Set<Integer>) - Method in class net.sourceforge.seqware.common.model.Study
-
Short-circuit permission checking by providing a set of entities that have already been checked
- givesPermissionInternal(Registration, Set<Integer>) - Method in class net.sourceforge.seqware.common.model.Workflow
-
Short-circuit permission checking by providing a set of entities that have already been checked
- givesPermissionInternal(Registration, Set<Integer>) - Method in class net.sourceforge.seqware.common.model.WorkflowParam
-
Short-circuit permission checking by providing a set of entities that have already been checked
- givesPermissionInternal(Registration, Set<Integer>) - Method in class net.sourceforge.seqware.common.model.WorkflowParamValue
-
Short-circuit permission checking by providing a set of entities that have already been checked
- givesPermissionInternal(Registration, Set<Integer>) - Method in class net.sourceforge.seqware.common.model.WorkflowRun
-
Short-circuit permission checking by providing a set of entities that have already been checked
- givesPermissionInternal(Registration, Set<Integer>) - Method in class net.sourceforge.seqware.common.model.WorkflowRunParam
-
Short-circuit permission checking by providing a set of entities that have already been checked
- givesPermissionInternal(Registration, Set<Integer>) - Method in class net.sourceforge.seqware.common.security.PermissionsAware
-
Short-circuit permission checking by providing a set of entities that have already been checked
- gridProxyInit() - Static method in class net.sourceforge.seqware.pipeline.workflow.BasicWorkflow
-
- s3ConnectionTimeout - Variable in class net.sourceforge.seqware.pipeline.modules.utilities.ProvisionFiles
-
- S3CreateFileURLs - Class in net.sourceforge.seqware.pipeline.modules.utilities
-
Purpose:
This module simply lists files at the S3 URL you provide and creates temporary URLs that can be shared
with others.
- S3CreateFileURLs() - Constructor for class net.sourceforge.seqware.pipeline.modules.utilities.S3CreateFileURLs
-
- S3DeleteFiles - Class in net.sourceforge.seqware.pipeline.modules.utilities
-
Purpose:
This module simply lists files at the S3 URL you provide.
- S3DeleteFiles() - Constructor for class net.sourceforge.seqware.pipeline.modules.utilities.S3DeleteFiles
-
- S3ListFiles - Class in net.sourceforge.seqware.pipeline.modules.utilities
-
Purpose:
This module simply lists files at the S3 URL you provide.
- S3ListFiles() - Constructor for class net.sourceforge.seqware.pipeline.modules.utilities.S3ListFiles
-
- s3MaxConnections - Variable in class net.sourceforge.seqware.pipeline.modules.utilities.ProvisionFiles
-
- s3MaxErrorRetry - Variable in class net.sourceforge.seqware.pipeline.modules.utilities.ProvisionFiles
-
- s3SocketTimeout - Variable in class net.sourceforge.seqware.pipeline.modules.utilities.ProvisionFiles
-
- S3UploadDirectory - Class in net.sourceforge.seqware.pipeline.modules.utilities
-
Purpose:
This module uses the Amazon API to recursively upload a directory to an S3
bucket.
- S3UploadDirectory() - Constructor for class net.sourceforge.seqware.pipeline.modules.utilities.S3UploadDirectory
-
- safe(String) - Static method in class net.sourceforge.seqware.common.util.Str
-
Returns a String suitable to be used in multiple contexts, e.g., as part of
a filename.
- Sample - Class in io.seqware.webservice.generated.model
-
- Sample() - Constructor for class io.seqware.webservice.generated.model.Sample
-
- Sample(Integer) - Constructor for class io.seqware.webservice.generated.model.Sample
-
- Sample(Integer, Date) - Constructor for class io.seqware.webservice.generated.model.Sample
-
- Sample - Class in net.sourceforge.seqware.common.model
-
- Sample() - Constructor for class net.sourceforge.seqware.common.model.Sample
-
Constructor for Sample.
- SAMPLE_ATTRIBUTES - Static variable in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles
-
Constant SAMPLE_ATTRIBUTES="Header.SAMPLE_ATTRIBUTES.getTitle()"
- SAMPLE_CHILD - Static variable in class net.sourceforge.solexatools.webapp.controller.StudyReportTableController
-
Constant SAMPLE_CHILD="s_child"
- SAMPLE_NAME - Static variable in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles
-
Constant SAMPLE_NAME="Header.SAMPLE_NAME.getTitle()"
- SAMPLE_PREFIX - Static variable in class net.sourceforge.solexatools.util.Constant
-
Constant SAMPLE_PREFIX="sam_"
- SAMPLE_SAMPLE - Static variable in class net.sourceforge.solexatools.webapp.controller.StudyReportTableController
-
Constant SAMPLE_SAMPLE="s_sample"
- SAMPLE_SWA - Static variable in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles
-
Constant SAMPLE_SWA="Header.SAMPLE_SWA.getTitle()"
- SAMPLE_SWID - Static variable in class net.sourceforge.solexatools.webapp.controller.SampleWorkflowRunsController
-
Constant SAMPLE_SWID="sw"
- SAMPLE_TAG_PREFIX - Static variable in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles
-
Constant SAMPLE_TAG_PREFIX="Header.SAMPLE_TAG_PREFIX.getTitle()"
- SampleAttribute - Class in io.seqware.webservice.generated.model
-
- SampleAttribute() - Constructor for class io.seqware.webservice.generated.model.SampleAttribute
-
- SampleAttribute(Integer) - Constructor for class io.seqware.webservice.generated.model.SampleAttribute
-
- SampleAttribute(Integer, String, String) - Constructor for class io.seqware.webservice.generated.model.SampleAttribute
-
- SampleAttribute - Class in net.sourceforge.seqware.common.model
-
SampleAttribute generated by hbm2java
- SampleAttribute() - Constructor for class net.sourceforge.seqware.common.model.SampleAttribute
-
Constructor for SampleAttribute.
- SampleAttribute(int, Sample, String, String) - Constructor for class net.sourceforge.seqware.common.model.SampleAttribute
-
Constructor for SampleAttribute.
- SampleAttribute(int, Sample, String, String, String) - Constructor for class net.sourceforge.seqware.common.model.SampleAttribute
-
Constructor for SampleAttribute.
- sampleAttributeAsDto(SampleAttribute) - Static method in class net.sourceforge.seqware.webservice.dto.Dtos
-
sampleAttributeAsDto.
- SampleAttributeDAO - Interface in net.sourceforge.seqware.common.dao
-
SampleAttributeDAO interface.
- SampleAttributeDAOHibernate - Class in net.sourceforge.seqware.common.dao.hibernate
-
SampleAttributeDAOHibernate class.
- SampleAttributeDAOHibernate() - Constructor for class net.sourceforge.seqware.common.dao.hibernate.SampleAttributeDAOHibernate
-
- SampleAttributeFacadeREST - Class in io.seqware.webservice.generated.controller
-
- SampleAttributeFacadeREST() - Constructor for class io.seqware.webservice.generated.controller.SampleAttributeFacadeREST
-
- SampleController - Class in net.sourceforge.solexatools.webapp.controller
-
SampleController
- SampleController() - Constructor for class net.sourceforge.solexatools.webapp.controller.SampleController
-
Constructor for SampleController.
- SampleController(Object) - Constructor for class net.sourceforge.solexatools.webapp.controller.SampleController
-
Constructor for SampleController.
- SampleDAO - Interface in net.sourceforge.seqware.common.dao
-
SampleDAO interface.
- SampleDAOHibernate - Class in net.sourceforge.seqware.common.dao.hibernate
-
SampleDAOHibernate class.
- SampleDAOHibernate() - Constructor for class net.sourceforge.seqware.common.dao.hibernate.SampleDAOHibernate
-
Constructor for SampleDAOHibernate.
- SampleDetailsLineItem - Class in net.sourceforge.solexatools.webapp.metamodel
-
SampleDetailsLineItem class.
- SampleDetailsLineItem(SequencerRun, Lane, IUS) - Constructor for class net.sourceforge.solexatools.webapp.metamodel.SampleDetailsLineItem
-
Constructor for SampleDetailsLineItem.
- SampleDetailsWorkflowLineItems - Class in net.sourceforge.solexatools.webapp.metamodel
-
SampleDetailsWorkflowLineItems class.
- SampleDetailsWorkflowLineItems(Sample) - Constructor for class net.sourceforge.solexatools.webapp.metamodel.SampleDetailsWorkflowLineItems
-
Constructor for SampleDetailsWorkflowLineItems.
- SampleDetailsWorkflowLineItems(Processing) - Constructor for class net.sourceforge.solexatools.webapp.metamodel.SampleDetailsWorkflowLineItems
-
Constructor for SampleDetailsWorkflowLineItems.
- SampleFacadeREST - Class in io.seqware.webservice.generated.controller
-
- SampleFacadeREST() - Constructor for class io.seqware.webservice.generated.controller.SampleFacadeREST
-
- SampleHierarchies - Class in net.sourceforge.seqware.queryengine.webservice.model
-
- SampleHierarchies() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.SampleHierarchies
-
- SampleHierarchy - Class in net.sourceforge.seqware.queryengine.webservice.model
-
- SampleHierarchy() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.SampleHierarchy
-
- SampleHierarchyPlugin - Class in net.sourceforge.seqware.pipeline.plugins.checkdb.plugins
-
Checks the metadb for issues specifically with the sample hierarchy.
- SampleHierarchyPlugin() - Constructor for class net.sourceforge.seqware.pipeline.plugins.checkdb.plugins.SampleHierarchyPlugin
-
- SampleHierarchyResource - Class in net.sourceforge.seqware.webservice.resources.queries
-
- SampleHierarchyResource(Context) - Constructor for class net.sourceforge.seqware.webservice.resources.queries.SampleHierarchyResource
-
- SampleIdFilesResource - Class in net.sourceforge.seqware.webservice.resources.queries
-
SampleIdFilesResource class.
- SampleIdFilesResource(Context) - Constructor for class net.sourceforge.seqware.webservice.resources.queries.SampleIdFilesResource
-
Constructor for SampleIdFilesResource.
- SampleIDFilter - Class in net.sourceforge.seqware.webservice.resources.filters
-
SampleIDFilter class.
- SampleIDFilter() - Constructor for class net.sourceforge.seqware.webservice.resources.filters.SampleIDFilter
-
- SampleIDResource - Class in net.sourceforge.seqware.webservice.resources.tables
-
SampleIDResource class.
- SampleIDResource() - Constructor for class net.sourceforge.seqware.webservice.resources.tables.SampleIDResource
-
Constructor for SampleIDResource.
- SampleInfo - Class in net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection
-
- SampleInfo() - Constructor for class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.SampleInfo
-
- SampleLink - Class in io.seqware.webservice.generated.model
-
- SampleLink() - Constructor for class io.seqware.webservice.generated.model.SampleLink
-
- SampleLink(Integer) - Constructor for class io.seqware.webservice.generated.model.SampleLink
-
- SampleLink(Integer, String, String) - Constructor for class io.seqware.webservice.generated.model.SampleLink
-
- SampleLink - Class in net.sourceforge.seqware.common.model
-
SampleLink generated by hbm2java
- SampleLink() - Constructor for class net.sourceforge.seqware.common.model.SampleLink
-
Constructor for SampleLink.
- SampleLink(int, Sample, String, String) - Constructor for class net.sourceforge.seqware.common.model.SampleLink
-
Constructor for SampleLink.
- SampleLink(int, Sample, String, String, String, String) - Constructor for class net.sourceforge.seqware.common.model.SampleLink
-
Constructor for SampleLink.
- SampleLinkDAO - Interface in net.sourceforge.seqware.common.dao
-
SampleLinkDAO interface.
- SampleLinkDAOHibernate - Class in net.sourceforge.seqware.common.dao.hibernate
-
SampleLinkDAOHibernate class.
- SampleLinkDAOHibernate() - Constructor for class net.sourceforge.seqware.common.dao.hibernate.SampleLinkDAOHibernate
-
- SampleLinkFacadeREST - Class in io.seqware.webservice.generated.controller
-
- SampleLinkFacadeREST() - Constructor for class io.seqware.webservice.generated.controller.SampleLinkFacadeREST
-
- SampleList - Class in net.sourceforge.seqware.common.model.lists
-
SampleList class.
- SampleList() - Constructor for class net.sourceforge.seqware.common.model.lists.SampleList
-
Constructor for SampleList.
- SampleRelationship - Class in io.seqware.webservice.generated.model
-
- SampleRelationship() - Constructor for class io.seqware.webservice.generated.model.SampleRelationship
-
- SampleRelationship(Integer) - Constructor for class io.seqware.webservice.generated.model.SampleRelationship
-
- SampleRelationshipFacadeREST - Class in io.seqware.webservice.generated.controller
-
- SampleRelationshipFacadeREST() - Constructor for class io.seqware.webservice.generated.controller.SampleRelationshipFacadeREST
-
- SampleReport - Class in io.seqware.webservice.generated.model
-
- SampleReport() - Constructor for class io.seqware.webservice.generated.model.SampleReport
-
- SampleReport(Integer) - Constructor for class io.seqware.webservice.generated.model.SampleReport
-
- SampleReportDAO - Interface in net.sourceforge.seqware.common.dao
-
SampleReportDAO interface.
- SampleReportDAOHibernate - Class in net.sourceforge.seqware.common.dao.hibernate
-
SampleReportDAOHibernate class.
- SampleReportDAOHibernate() - Constructor for class net.sourceforge.seqware.common.dao.hibernate.SampleReportDAOHibernate
-
- SampleReportFacadeREST - Class in io.seqware.webservice.generated.controller
-
- SampleReportFacadeREST() - Constructor for class io.seqware.webservice.generated.controller.SampleReportFacadeREST
-
- SampleReportRow - Class in net.sourceforge.seqware.common.model
-
SampleReportRow class.
- SampleReportRow() - Constructor for class net.sourceforge.seqware.common.model.SampleReportRow
-
- SampleReportService - Interface in net.sourceforge.seqware.common.business
-
SampleReportService interface.
- SampleReportService.Status - Enum in net.sourceforge.seqware.common.business
-
- SampleReportServiceImpl - Class in net.sourceforge.seqware.common.business.impl
-
SampleReportServiceImpl class.
- SampleReportServiceImpl() - Constructor for class net.sourceforge.seqware.common.business.impl.SampleReportServiceImpl
-
- SampleResource - Class in net.sourceforge.seqware.webservice.resources.tables
-
SampleResource class.
- SampleResource() - Constructor for class net.sourceforge.seqware.webservice.resources.tables.SampleResource
-
Constructor for SampleResource.
- SampleSearch - Class in io.seqware.webservice.generated.model
-
- SampleSearch() - Constructor for class io.seqware.webservice.generated.model.SampleSearch
-
- SampleSearch(Integer) - Constructor for class io.seqware.webservice.generated.model.SampleSearch
-
- SampleSearch(Integer, Date) - Constructor for class io.seqware.webservice.generated.model.SampleSearch
-
- SampleSearch - Class in net.sourceforge.seqware.common.model
-
A search for samples that match a given list of attributes.
- SampleSearch() - Constructor for class net.sourceforge.seqware.common.model.SampleSearch
-
- SampleSearchAttribute - Class in io.seqware.webservice.generated.model
-
- SampleSearchAttribute() - Constructor for class io.seqware.webservice.generated.model.SampleSearchAttribute
-
- SampleSearchAttribute(Integer) - Constructor for class io.seqware.webservice.generated.model.SampleSearchAttribute
-
- SampleSearchAttribute(Integer, String, String) - Constructor for class io.seqware.webservice.generated.model.SampleSearchAttribute
-
- SampleSearchAttribute - Class in net.sourceforge.seqware.common.model
-
Attributes that are part of a sample search.
- SampleSearchAttribute() - Constructor for class net.sourceforge.seqware.common.model.SampleSearchAttribute
-
- SampleSearchAttributeFacadeREST - Class in io.seqware.webservice.generated.controller
-
- SampleSearchAttributeFacadeREST() - Constructor for class io.seqware.webservice.generated.controller.SampleSearchAttributeFacadeREST
-
- SampleSearchDAO - Interface in net.sourceforge.seqware.common.dao
-
SampleSearchDAO interface.
- SampleSearchDAOHibernate - Class in net.sourceforge.seqware.common.dao.hibernate
-
- SampleSearchDAOHibernate() - Constructor for class net.sourceforge.seqware.common.dao.hibernate.SampleSearchDAOHibernate
-
- SampleSearchDto - Class in net.sourceforge.seqware.webservice.dto
-
- SampleSearchDto() - Constructor for class net.sourceforge.seqware.webservice.dto.SampleSearchDto
-
- SampleSearchFacadeREST - Class in io.seqware.webservice.generated.controller
-
- SampleSearchFacadeREST() - Constructor for class io.seqware.webservice.generated.controller.SampleSearchFacadeREST
-
- SampleSearchService - Interface in net.sourceforge.seqware.common.business
-
SampleSearchService interface.
- SampleSearchServiceImpl - Class in net.sourceforge.seqware.common.business.impl
-
- SampleSearchServiceImpl() - Constructor for class net.sourceforge.seqware.common.business.impl.SampleSearchServiceImpl
-
- SampleService - Interface in net.sourceforge.seqware.common.business
-
SampleService interface.
- SampleServiceImpl - Class in net.sourceforge.seqware.common.business.impl
-
SampleServiceImpl class.
- SampleServiceImpl() - Constructor for class net.sourceforge.seqware.common.business.impl.SampleServiceImpl
-
Constructor for SampleServiceImpl.
- SampleSetupController - Class in net.sourceforge.solexatools.webapp.controller
-
RegistrationSetupController
- SampleSetupController() - Constructor for class net.sourceforge.solexatools.webapp.controller.SampleSetupController
-
Constructor for SampleSetupController.
- SampleValidator - Class in net.sourceforge.solexatools.validation
-
SampleValidator class.
- SampleValidator() - Constructor for class net.sourceforge.solexatools.validation.SampleValidator
-
Constructor for SampleValidator.
- SampleWorkflowRunsController - Class in net.sourceforge.solexatools.webapp.controller
-
SampleWorkflowRunsController class.
- SampleWorkflowRunsController() - Constructor for class net.sourceforge.solexatools.webapp.controller.SampleWorkflowRunsController
-
- SanityCheck - Class in io.seqware.pipeline.plugins.sanity
-
A database validation tool for your SeqWare metadb
- SanityCheck() - Constructor for class io.seqware.pipeline.plugins.sanity.SanityCheck
-
Constructor for HelloWorld.
- SanityCheckPluginInterface - Interface in io.seqware.pipeline.plugins.sanity
-
Specifies an interface for checks that can be done for a SeqWare install
- saveAscInSession(HttpServletRequest, String) - Static method in class net.sourceforge.solexatools.util.ControllerUtil
-
saveAscInSession.
- saveAscInSession(HttpServletRequest, String) - Method in class net.sourceforge.solexatools.webapp.controller.StudyListDetailsController
-
saveAscInSession.
- saveFile(MultipartFile, String, Registration) - Method in interface net.sourceforge.seqware.common.dao.FileDAO
-
saveFile.
- saveFile(MultipartFile, String, Registration) - Method in class net.sourceforge.seqware.common.dao.hibernate.FileDAOHibernate
-
saveFile.
- saveFileForIus(int, int, FileMetadata, int) - Method in interface net.sourceforge.seqware.common.metadata.Metadata
-
saveFileForIus.
- saveFileForIus(int, int, FileMetadata, int) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
-
saveFileForIus.
- saveFileForIus(int, int, FileMetadata, int) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection
-
saveFileForIus.
- saveFileForIus(int, int, FileMetadata, int) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS
-
saveFileForIus.
- SaveOpenNodeController - Class in net.sourceforge.solexatools.webapp.controller
-
SaveOpenNodeController class.
- SaveOpenNodeController() - Constructor for class net.sourceforge.solexatools.webapp.controller.SaveOpenNodeController
-
Constructor for SaveOpenNodeController.
- saveSelectedWorkflowParamValue(HttpServletRequest, Integer, String) - Static method in class net.sourceforge.solexatools.util.LaunchWorkflowUtil
-
saveSelectedWorkflowParamValue.
- SCHEDULE - Static variable in class net.sourceforge.seqware.pipeline.plugin.WorkflowPlugin
-
- scheduleInstalledBundle(String, String, ArrayList<String>, boolean, ArrayList<String>, ArrayList<String>, boolean, List<String>) - Method in class net.sourceforge.seqware.pipeline.workflow.BasicWorkflow
-
scheduleInstalledBundle.
- scheduleInstalledBundle(String, String, ArrayList<String>, boolean, ArrayList<String>, ArrayList<String>, boolean, List<String>, String, String, Set<Integer>) - Method in class net.sourceforge.seqware.pipeline.workflow.BasicWorkflow
-
This method just needs a sw_accession value from the workflow table and an
ini file(s) in order to schedule a workflow.
- scheduleInstalledBundle(String, String, ArrayList<String>, boolean, ArrayList<String>, ArrayList<String>, boolean, List<String>) - Method in interface net.sourceforge.seqware.pipeline.workflowV2.WorkflowEngine
-
scheduleInstalledBundle.
- scheduleWorkflowRun(int, String, String, String, String, String, String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.MetadataDB
-
scheduleWorkflowRun.
- Script_Check - Class in io.seqware.pipeline.plugins.sanity.checks
-
Runs through our CLI tutorial
- Script_Check() - Constructor for class io.seqware.pipeline.plugins.sanity.checks.Script_Check
-
- scriptFileName(String) - Static method in class net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object.OozieBashJob
-
- SCRIPTS_SUBDIR - Static variable in class net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object.OozieJob
-
The sub-directory (of the working directory) in which generated script
files will be placed.
- scriptsDir - Variable in class net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object.OozieJob
-
- scriptsDir(String) - Static method in class net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object.OozieJob
-
- SEARCH_CASE_SENSITIVE - Static variable in class net.sourceforge.solexatools.webapp.controller.SearchController
-
Constant SEARCH_CASE_SENSITIVE="search.checked"
- SearchController - Class in net.sourceforge.solexatools.webapp.controller
-
SearchController class.
- SearchController() - Constructor for class net.sourceforge.solexatools.webapp.controller.SearchController
-
Constructor for SearchController.
- SearchResultsController - Class in net.sourceforge.solexatools.webapp.controller
-
SearchResultsController class.
- SearchResultsController() - Constructor for class net.sourceforge.solexatools.webapp.controller.SearchResultsController
-
- SearchResultsListController - Class in net.sourceforge.solexatools.webapp.controller
-
SearchResultsListController class.
- SearchResultsListController() - Constructor for class net.sourceforge.solexatools.webapp.controller.SearchResultsListController
-
Constructor for SearchResultsListController.
- SecondTierModel - Interface in net.sourceforge.seqware.common.model
-
This links together all models that do not have sw_accession
- secretKey - Variable in class net.sourceforge.seqware.pipeline.modules.utilities.S3CreateFileURLs
-
- secretKey - Variable in class net.sourceforge.seqware.pipeline.modules.utilities.S3DeleteFiles
-
- secretKey - Variable in class net.sourceforge.seqware.pipeline.modules.utilities.S3ListFiles
-
- Security - Class in net.sourceforge.solexatools
-
Security class.
- Security() - Constructor for class net.sourceforge.solexatools.Security
-
- SELECTED_FILES - Static variable in class net.sourceforge.solexatools.util.LaunchWorkflowUtil
-
Constant SELECTED_FILES="selectedLaunchFiles"
- SELECTED_NODES - Static variable in class net.sourceforge.solexatools.util.LaunchWorkflowUtil
-
Constant SELECTED_NODES="launchSelectedNodes"
- SELECTED_VALUES - Static variable in class net.sourceforge.solexatools.util.LaunchWorkflowUtil
-
Constant SELECTED_VALUES="selectedWorkflowParamValueId"
- selectExperimentNode(List<String>, Study) - Static method in class net.sourceforge.solexatools.util.BulkUtil
-
selectExperimentNode.
- SelectInputController - Class in net.sourceforge.solexatools.webapp.controller
-
SelectInputController class.
- SelectInputController() - Constructor for class net.sourceforge.solexatools.webapp.controller.SelectInputController
-
Constructor for SelectInputController.
- SelectInputController(Object) - Constructor for class net.sourceforge.solexatools.webapp.controller.SelectInputController
-
Constructor for SelectInputController.
- SelectInputListController - Class in net.sourceforge.solexatools.webapp.controller
-
SelectInputListController class.
- SelectInputListController() - Constructor for class net.sourceforge.solexatools.webapp.controller.SelectInputListController
-
Constructor for SelectInputListController.
- selectIUSNode(List<String>, Sample) - Static method in class net.sourceforge.solexatools.util.BulkUtil
-
selectIUSNode.
- selectProcessingNode(List<String>, WorkflowRun) - Static method in class net.sourceforge.solexatools.util.BulkUtil
-
selectProcessingNode.
- selectProcessingNode(List<String>, Processing) - Static method in class net.sourceforge.solexatools.util.BulkUtil
-
selectProcessingNode.
- selectProcessingNode(List<String>, Lane) - Static method in class net.sourceforge.solexatools.util.BulkUtil
-
selectProcessingNode.
- selectProcessingNode(List<String>, IUS) - Static method in class net.sourceforge.solexatools.util.BulkUtil
-
selectProcessingNode.
- SelectQueryRunner - Class in net.sourceforge.seqware.pipeline.plugins.checkdb
-
A class that allows plugin writers to only do select queries
without any risk of leaving open connections or other unfriendliness
- SelectQueryRunner(MetadataDB) - Constructor for class net.sourceforge.seqware.pipeline.plugins.checkdb.SelectQueryRunner
-
- selectSampleNode(List<String>, Experiment) - Static method in class net.sourceforge.solexatools.util.BulkUtil
-
selectSampleNode.
- selectStudyNode(List<String>, List<Study>) - Static method in class net.sourceforge.solexatools.util.BulkUtil
-
selectStudyNode.
- selectWorkflowRunNode(List<String>, List<WorkflowRun>) - Static method in class net.sourceforge.solexatools.util.BulkUtil
-
selectWorkflowRunNode.
- separateFiles(List<ReturnValue>, String) - Method in class net.sourceforge.seqware.pipeline.deciders.BasicDecider
-
- SEPARATOR - Static variable in class net.sourceforge.solexatools.webapp.controller.ChangeNumberPopupPageController
-
Constant SEPARATOR="java.io.File.separator"
- SEPARATOR - Static variable in class net.sourceforge.solexatools.webapp.controller.DeleteLoadedIndexPageController
-
Constant SEPARATOR="java.io.File.separator"
- SEQ_RUN_ID - Static variable in class net.sourceforge.solexatools.webapp.controller.SequencerRunReportTableController
-
Constant SEQ_RUN_ID="seq_run_id"
- SEQUENCER_RUN_ATTRIBUTES - Static variable in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles
-
Constant SEQUENCER_RUN_ATTRIBUTES="Header.SEQUENCER_RUN_ATTRIBUTES.getTitl"{trunked}
- SEQUENCER_RUN_NAME - Static variable in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles
-
Constant SEQUENCER_RUN_NAME="Header.SEQUENCER_RUN_NAME.getTitle()"
- SEQUENCER_RUN_SWA - Static variable in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles
-
Constant SEQUENCER_RUN_SWA="Header.SEQUENCER_RUN_SWA.getTitle()"
- SEQUENCER_RUN_TAG_PREFIX - Static variable in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles
-
Constant SEQUENCER_RUN_TAG_PREFIX="Header.SEQUENCER_RUN_TAG_PREFIX.getTitl"{trunked}
- SEQUENCER_VIEW - Static variable in class net.sourceforge.solexatools.util.Constant
-
Constant SEQUENCER_VIEW="redirect:/sequencerRunList.htm"
- SequencerRun - Class in io.seqware.webservice.generated.model
-
- SequencerRun() - Constructor for class io.seqware.webservice.generated.model.SequencerRun
-
- SequencerRun(Integer) - Constructor for class io.seqware.webservice.generated.model.SequencerRun
-
- SequencerRun(Integer, Date) - Constructor for class io.seqware.webservice.generated.model.SequencerRun
-
- SequencerRun - Class in net.sourceforge.seqware.common.model
-
- SequencerRun() - Constructor for class net.sourceforge.seqware.common.model.SequencerRun
-
Constructor for SequencerRun.
- SequencerRunAttribute - Class in io.seqware.webservice.generated.model
-
- SequencerRunAttribute() - Constructor for class io.seqware.webservice.generated.model.SequencerRunAttribute
-
- SequencerRunAttribute(Integer) - Constructor for class io.seqware.webservice.generated.model.SequencerRunAttribute
-
- SequencerRunAttribute(Integer, String, String) - Constructor for class io.seqware.webservice.generated.model.SequencerRunAttribute
-
- SequencerRunAttribute - Class in net.sourceforge.seqware.common.model
-
SequencerRunAttribute generated by Morgan Taschuk
- SequencerRunAttribute() - Constructor for class net.sourceforge.seqware.common.model.SequencerRunAttribute
-
Constructor for SequencerRunAttribute.
- SequencerRunAttribute(int, SequencerRunWizardDTO) - Constructor for class net.sourceforge.seqware.common.model.SequencerRunAttribute
-
Constructor for SequencerRunAttribute.
- SequencerRunAttribute(int, SequencerRunWizardDTO, String, String, String) - Constructor for class net.sourceforge.seqware.common.model.SequencerRunAttribute
-
Constructor for SequencerRunAttribute.
- SequencerRunAttributeFacadeREST - Class in io.seqware.webservice.generated.controller
-
- SequencerRunAttributeFacadeREST() - Constructor for class io.seqware.webservice.generated.controller.SequencerRunAttributeFacadeREST
-
- SequencerRunController - Class in net.sourceforge.solexatools.webapp.controller
-
SequencerRunController
- SequencerRunController() - Constructor for class net.sourceforge.solexatools.webapp.controller.SequencerRunController
-
Constructor for SequencerRunController.
- SequencerRunController(Object) - Constructor for class net.sourceforge.solexatools.webapp.controller.SequencerRunController
-
Constructor for SequencerRunController.
- SequencerRunControllerDTO - Class in net.sourceforge.solexatools.webapp.controller
-
SequencerRunController
- SequencerRunControllerDTO() - Constructor for class net.sourceforge.solexatools.webapp.controller.SequencerRunControllerDTO
-
Constructor for SequencerRunControllerDTO.
- SequencerRunControllerDTO(Object) - Constructor for class net.sourceforge.solexatools.webapp.controller.SequencerRunControllerDTO
-
Constructor for SequencerRunControllerDTO.
- SequencerRunDAO - Interface in net.sourceforge.seqware.common.dao
-
SequencerRunDAO interface.
- SequencerRunDAOHibernate - Class in net.sourceforge.seqware.common.dao.hibernate
-
SequencerRunDAOHibernate class.
- SequencerRunDAOHibernate() - Constructor for class net.sourceforge.seqware.common.dao.hibernate.SequencerRunDAOHibernate
-
Constructor for SequencerRunDAOHibernate.
- SequencerRunDTO - Class in net.sourceforge.seqware.common.model
-
- SequencerRunDTO() - Constructor for class net.sourceforge.seqware.common.model.SequencerRunDTO
-
Constructor for SequencerRunDTO.
- SequencerRunFacadeREST - Class in io.seqware.webservice.generated.controller
-
- SequencerRunFacadeREST() - Constructor for class io.seqware.webservice.generated.controller.SequencerRunFacadeREST
-
- SequencerRunHtmlUtil - Class in net.sourceforge.solexatools.util
-
SequencerRunHtmlUtil class.
- SequencerRunHtmlUtil() - Constructor for class net.sourceforge.solexatools.util.SequencerRunHtmlUtil
-
- SequencerRunIdFilesResource - Class in net.sourceforge.seqware.webservice.resources.queries
-
SequencerRunIdFilesResource class.
- SequencerRunIdFilesResource(Context) - Constructor for class net.sourceforge.seqware.webservice.resources.queries.SequencerRunIdFilesResource
-
Constructor for SequencerRunIdFilesResource.
- SequencerRunIDResource - Class in net.sourceforge.seqware.webservice.resources.tables
-
SequencerRunIDResource class.
- SequencerRunIDResource() - Constructor for class net.sourceforge.seqware.webservice.resources.tables.SequencerRunIDResource
-
Constructor for SequencerRunIDResource.
- SequencerRunList - Class in net.sourceforge.seqware.common.model.lists
-
SequencerRunList class.
- SequencerRunList() - Constructor for class net.sourceforge.seqware.common.model.lists.SequencerRunList
-
Constructor for SequencerRunList.
- SequencerRunListController - Class in net.sourceforge.solexatools.webapp.controller
-
RegistrationSetupController
- SequencerRunListController() - Constructor for class net.sourceforge.solexatools.webapp.controller.SequencerRunListController
-
Constructor for SequencerRunListController.
- SequencerRunListDetailsController - Class in net.sourceforge.solexatools.webapp.controller
-
SequencerRunListDetailsController class.
- SequencerRunListDetailsController() - Constructor for class net.sourceforge.solexatools.webapp.controller.SequencerRunListDetailsController
-
Constructor for SequencerRunListDetailsController.
- SequencerRunReport - Class in net.sourceforge.seqware.common.hibernate
-
SequencerRunReport class.
- SequencerRunReport() - Constructor for class net.sourceforge.seqware.common.hibernate.SequencerRunReport
-
- SequencerRunReport.Row - Class in net.sourceforge.seqware.common.hibernate
-
- SequencerRunReport.Row(Date, String, String, String, String, String, String, String, String) - Constructor for class net.sourceforge.seqware.common.hibernate.SequencerRunReport.Row
-
- SequencerRunReporter - Class in net.sourceforge.seqware.pipeline.plugins
-
SequencerRunReporter class.
- SequencerRunReporter() - Constructor for class net.sourceforge.seqware.pipeline.plugins.SequencerRunReporter
-
Constructor for SequencerRunReporter.
- SequencerRunReportId - Class in net.sourceforge.seqware.common.model
-
SequencerRunReportId class.
- SequencerRunReportId() - Constructor for class net.sourceforge.seqware.common.model.SequencerRunReportId
-
- SequencerRunReportResource - Class in net.sourceforge.seqware.webservice.resources.queries
-
SequencerRunReportResource class.
- SequencerRunReportResource(Context) - Constructor for class net.sourceforge.seqware.webservice.resources.queries.SequencerRunReportResource
-
Constructor for SequencerRunReportResource.
- SequencerRunReportSetupController - Class in net.sourceforge.solexatools.webapp.controller
-
- SequencerRunReportSetupController() - Constructor for class net.sourceforge.solexatools.webapp.controller.SequencerRunReportSetupController
-
- SequencerRunReportTableController - Class in net.sourceforge.solexatools.webapp.controller
-
- SequencerRunReportTableController() - Constructor for class net.sourceforge.solexatools.webapp.controller.SequencerRunReportTableController
-
- SequencerRunResource - Class in net.sourceforge.seqware.webservice.resources.tables
-
SequencerRunResource class.
- SequencerRunResource() - Constructor for class net.sourceforge.seqware.webservice.resources.tables.SequencerRunResource
-
Constructor for SequencerRunResource.
- SequencerRunService - Interface in net.sourceforge.seqware.common.business
-
SequencerRunService interface.
- SequencerRunServiceImpl - Class in net.sourceforge.seqware.common.business.impl
-
SequencerRunServiceImpl class.
- SequencerRunServiceImpl() - Constructor for class net.sourceforge.seqware.common.business.impl.SequencerRunServiceImpl
-
Constructor for SequencerRunServiceImpl.
- SequencerRunSetupController - Class in net.sourceforge.solexatools.webapp.controller
-
SequencingRunSetupController
- SequencerRunSetupController() - Constructor for class net.sourceforge.solexatools.webapp.controller.SequencerRunSetupController
-
Constructor for SequencerRunSetupController.
- SequencerRunSetupControllerDTO - Class in net.sourceforge.solexatools.webapp.controller
-
SequencingRunSetupController
- SequencerRunSetupControllerDTO() - Constructor for class net.sourceforge.solexatools.webapp.controller.SequencerRunSetupControllerDTO
-
Constructor for SequencerRunSetupControllerDTO.
- SequencerRunStatus - Enum in net.sourceforge.seqware.common.model
-
- SequencerRunValidator - Class in net.sourceforge.solexatools.validation
-
SequencerRunValidator class.
- SequencerRunValidator() - Constructor for class net.sourceforge.solexatools.validation.SequencerRunValidator
-
Constructor for SequencerRunValidator.
- SequencerRunWizardController - Class in net.sourceforge.solexatools.webapp.controller
-
SequencerRunWizardController class.
- SequencerRunWizardController() - Constructor for class net.sourceforge.solexatools.webapp.controller.SequencerRunWizardController
-
Constructor for SequencerRunWizardController.
- SequencerRunWizardController(Object) - Constructor for class net.sourceforge.solexatools.webapp.controller.SequencerRunWizardController
-
Constructor for SequencerRunWizardController.
- SequencerRunWizardDTO - Class in net.sourceforge.seqware.common.model
-
SequencerRunWizardDTO class.
- SequencerRunWizardDTO() - Constructor for class net.sourceforge.seqware.common.model.SequencerRunWizardDTO
-
Constructor for SequencerRunWizardDTO.
- SequencerRunWizardSetupController - Class in net.sourceforge.solexatools.webapp.controller
-
RegistrationSetupController
This is invoked upon entry to Registration.jsp or RegistrationUpdate.jsp
- SequencerRunWizardSetupController() - Constructor for class net.sourceforge.solexatools.webapp.controller.SequencerRunWizardSetupController
-
Constructor for SequencerRunWizardSetupController.
- SequencerRunWizardValidator - Class in net.sourceforge.solexatools.validation
-
SequencerRunWizardValidator class.
- SequencerRunWizardValidator() - Constructor for class net.sourceforge.solexatools.validation.SequencerRunWizardValidator
-
Constructor for SequencerRunWizardValidator.
- SEQWARE_SETTINGS_PROPERTY - Static variable in class net.sourceforge.seqware.common.util.configtools.ConfigTools
-
Constant SEQWARE_SETTINGS_PROPERTY="SEQWARE_SETTINGS"
- SeqwareAccessionIDResource - Class in net.sourceforge.seqware.webservice.resources
-
SeqwareAccessionIDResource class.
- SeqwareAccessionIDResource() - Constructor for class net.sourceforge.seqware.webservice.resources.SeqwareAccessionIDResource
-
- SeqwareAccessionResource - Class in net.sourceforge.seqware.webservice.resources
-
SeqwareAccessionResource class.
- SeqwareAccessionResource() - Constructor for class net.sourceforge.seqware.webservice.resources.SeqwareAccessionResource
-
- SeqwareException - Exception in net.sourceforge.seqware.common.err
-
Created by IntelliJ IDEA.
- SeqwareException() - Constructor for exception net.sourceforge.seqware.common.err.SeqwareException
-
Constructor for SeqwareException.
- SeqwareException(String) - Constructor for exception net.sourceforge.seqware.common.err.SeqwareException
-
Constructor for SeqwareException.
- SeqwareException(String, Throwable) - Constructor for exception net.sourceforge.seqware.common.err.SeqwareException
-
Constructor for SeqwareException.
- SeqwareException(Throwable) - Constructor for exception net.sourceforge.seqware.common.err.SeqwareException
-
Constructor for SeqwareException.
- SeqwareExitCode - Class in net.sourceforge.seqware.common.err
-
Created by IntelliJ IDEA.
- SeqwareExitCode() - Constructor for class net.sourceforge.seqware.common.err.SeqwareExitCode
-
- seqwareJar - Variable in class net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object.OozieJob
-
- seqwareJarPath - Variable in class net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object.OozieJob
-
- seqwareJarPath(AbstractWorkflowDataModel) - Static method in class net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.OozieWorkflowEngine
-
- SeqWareVerifier - Class in net.sourceforge.seqware.queryengine.webservice.security
-
SeqWareVerifier class.
- SeqWareVerifier() - Constructor for class net.sourceforge.seqware.queryengine.webservice.security.SeqWareVerifier
-
- SeqWareWebServiceApplication - Class in net.sourceforge.seqware.queryengine.webservice.controller
-
SeqWareWebServiceApplication class.
- SeqWareWebServiceApplication() - Constructor for class net.sourceforge.seqware.queryengine.webservice.controller.SeqWareWebServiceApplication
-
- SeqWareWebServiceApplication.OptionalSlashRedirect - Class in net.sourceforge.seqware.queryengine.webservice.controller
-
http://restlet-discuss.1400322.n2.nabble.com/Proper-handling-of-at-the-end-of-the-requested-URI-td5819896.html
- SeqWareWebServiceApplication.OptionalSlashRedirect(Context) - Constructor for class net.sourceforge.seqware.queryengine.webservice.controller.SeqWareWebServiceApplication.OptionalSlashRedirect
-
- SeqWareWebServiceApplication.OptionalSlashRedirect() - Constructor for class net.sourceforge.seqware.queryengine.webservice.controller.SeqWareWebServiceApplication.OptionalSlashRedirect
-
- SeqWareWebServiceApplicationVersion - Class in net.sourceforge.seqware.queryengine.webservice.controller
-
SeqWareWebServiceApplicationVersion class.
- SeqWareWebServiceApplicationVersion() - Constructor for class net.sourceforge.seqware.queryengine.webservice.controller.SeqWareWebServiceApplicationVersion
-
- SeqWareWebServiceApplicationVersion.OptionalSlashRedirect - Class in net.sourceforge.seqware.queryengine.webservice.controller
-
http://restlet-discuss.1400322.n2.nabble.com/Proper-handling-of-at-the-end-of-the-requested-URI-td5819896.html
- SeqWareWebServiceApplicationVersion.OptionalSlashRedirect(Context) - Constructor for class net.sourceforge.seqware.queryengine.webservice.controller.SeqWareWebServiceApplicationVersion.OptionalSlashRedirect
-
- SeqWareWebServiceApplicationVersion.OptionalSlashRedirect() - Constructor for class net.sourceforge.seqware.queryengine.webservice.controller.SeqWareWebServiceApplicationVersion.OptionalSlashRedirect
-
- SeqWareWebServiceClient - Class in io.seqware.webservice.client
-
Separate custom code from base client that would be destroyed during a regeneration
- SeqWareWebServiceClient(String) - Constructor for class io.seqware.webservice.client.SeqWareWebServiceClient
-
Constructor that uses default baseURI
- SeqWareWebServiceClient(String, String) - Constructor for class io.seqware.webservice.client.SeqWareWebServiceClient
-
Constructs a SeqWare web service client for the given resource and url.
- SeqWareWebserviceClient - Class in io.seqware.webservice.generated.client
-
Jersey REST client generated for REST resource:OrganismFacadeREST
[io.seqware.webservice.model.organism]
USAGE:
- SeqWareWebserviceClient() - Constructor for class io.seqware.webservice.generated.client.SeqWareWebserviceClient
-
- SeqWareWebserviceClient(String) - Constructor for class io.seqware.webservice.generated.client.SeqWareWebserviceClient
-
Constructs a SeqWare web service client for the given resource and url.
- SeqWareWebServiceMain - Class in net.sourceforge.seqware.queryengine.webservice.controller
-
SeqWareWebServiceMain class.
- serializeXML() - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object.OozieJob
-
- serializeXML() - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object.WorkflowApp
-
- serializeXML() - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object.Adag
-
Adag object serialize to
element
and all its sub objects serialize to sub element
- serializeXML() - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object.PegasusJob
-
- serializeXML() - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object.Pfn
- serializeXML() - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object.WorkflowExecutable
-
- set_processing_update_tstmp_if_null(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
- setAbstract1(String) - Method in class io.seqware.webservice.generated.model.Study
-
- setAbstractStr(String) - Method in class net.sourceforge.seqware.common.model.Study
-
Setter for the field abstractStr.
- setAccession(int) - Method in class io.seqware.webservice.controller.ModelAccessionIDTuple
-
- setAccession(int) - Method in class io.seqware.webservice.generated.controller.ModelAccessionIDTuple
-
- setAccession(String) - Method in class io.seqware.webservice.generated.model.Experiment
-
- setAccession(String) - Method in class io.seqware.webservice.generated.model.Organism
-
- setAccession(String) - Method in class io.seqware.webservice.generated.model.Study
-
- setAccession(String) - Method in class net.sourceforge.seqware.common.model.Experiment
-
Setter for the field accession.
- setAccession(String) - Method in class net.sourceforge.seqware.common.model.Organism
-
Setter for the field accession.
- setAccession(String) - Method in class net.sourceforge.seqware.common.model.Study
-
Setter for the field accession.
- setActive(Boolean) - Method in class io.seqware.webservice.generated.model.ShareExperiment
-
- setActive(Boolean) - Method in class io.seqware.webservice.generated.model.ShareFile
-
- setActive(Boolean) - Method in class io.seqware.webservice.generated.model.ShareLane
-
- setActive(Boolean) - Method in class io.seqware.webservice.generated.model.ShareProcessing
-
- setActive(Boolean) - Method in class io.seqware.webservice.generated.model.ShareSample
-
- setActive(Boolean) - Method in class io.seqware.webservice.generated.model.ShareStudy
-
- setActive(Boolean) - Method in class io.seqware.webservice.generated.model.ShareWorkflowRun
-
- setActive(Boolean) - Method in class net.sourceforge.seqware.common.model.ShareExperiment
-
Setter for the field active.
- setActive(Boolean) - Method in class net.sourceforge.seqware.common.model.ShareFile
-
Setter for the field active.
- setActive(Boolean) - Method in class net.sourceforge.seqware.common.model.ShareLane
-
Setter for the field active.
- setActive(Boolean) - Method in class net.sourceforge.seqware.common.model.ShareProcessing
-
Setter for the field active.
- setActive(Boolean) - Method in class net.sourceforge.seqware.common.model.ShareSample
-
Setter for the field active.
- setActive(Boolean) - Method in class net.sourceforge.seqware.common.model.ShareStudy
-
Setter for the field active.
- setActive(Boolean) - Method in class net.sourceforge.seqware.common.model.ShareWorkflowRun
-
Setter for the field active.
- setAdapters(String) - Method in class io.seqware.webservice.generated.model.Sample
-
- setAdapters(String) - Method in class net.sourceforge.seqware.common.model.Sample
-
Setter for the field
adapters.
- setAdapterSpec(String) - Method in class io.seqware.webservice.generated.model.ExperimentSpotDesign
-
- setAdapterSpec(String) - Method in class net.sourceforge.seqware.common.model.ExperimentSpotDesign
-
Setter for the field adapterSpec.
- setAddedSurcharge(BigInteger) - Method in class io.seqware.webservice.generated.model.Expense
-
- setAddedSurcharge(Double) - Method in class net.sourceforge.seqware.common.model.Expense
-
Setter for the field
addedSurcharge.
- setAdminModelClass(String) - Method in class io.seqware.webservice.controller.ModelAccessionIDTuple
-
- setAdminModelClass(String) - Method in class io.seqware.webservice.generated.controller.ModelAccessionIDTuple
-
- setAgent(String) - Method in class io.seqware.webservice.generated.model.Expense
-
- setAgent(String) - Method in class net.sourceforge.seqware.common.model.Expense
-
Setter for the field
agent.
- setAlgo(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.AbstractJob
-
set the job algorithm
- setAlgorithm(String) - Method in class io.seqware.webservice.generated.model.Processing
-
- setAlgorithm(String) - Method in class net.sourceforge.seqware.common.model.Processing
-
Setter for the field algorithm.
- setAlgorithm(String) - Method in class net.sourceforge.seqware.common.module.ReturnValue
-
Setter for the field algorithm.
- setAlgorithm(String) - Method in class net.sourceforge.seqware.pipeline.module.Module
-
Setter for the field algorithm.
- setAlias(String) - Method in class io.seqware.webservice.generated.model.Experiment
-
- setAlias(String) - Method in class io.seqware.webservice.generated.model.Ius
-
- setAlias(String) - Method in class io.seqware.webservice.generated.model.Lane
-
- setAlias(String) - Method in class io.seqware.webservice.generated.model.Sample
-
- setAlias(String) - Method in class io.seqware.webservice.generated.model.Study
-
- setAlias(String) - Method in class net.sourceforge.seqware.common.model.Experiment
-
Setter for the field alias.
- setAlias(String) - Method in class net.sourceforge.seqware.common.model.IUS
-
Setter for the field alias.
- setAlias(String) - Method in class net.sourceforge.seqware.common.model.Sample
-
Setter for the field
alias.
- setAlias(String) - Method in class net.sourceforge.seqware.common.model.Study
-
Setter for the field alias.
- setAlign(String) - Method in class net.sourceforge.solexatools.webapp.metamodel.Flexigrid.ColumnModel
-
- setAllInputFiles(Collection<File>) - Method in class net.sourceforge.seqware.common.hibernate.reports.WorkflowRunReportRow
-
Setter for the field allInputFiles.
- setAllItems(String) - Method in class net.sourceforge.solexatools.util.PageInfo
-
Setter for the field allItems.
- setAncestorWorkflowRunId(WorkflowRun) - Method in class io.seqware.webservice.generated.model.Processing
-
- setAnonymizedName(String) - Method in class io.seqware.webservice.generated.model.Sample
-
- setAnonymizedName(String) - Method in class net.sourceforge.seqware.common.model.Sample
-
Setter for the field
anonymizedName.
- setArch(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object.WorkflowExecutable
-
- setArgs(String[]) - Method in class net.sourceforge.seqware.pipeline.tools.ReportTest.TestThread
-
- setArguments(List<String>) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Command
-
- setAssayType(String) - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.RunInfo
-
Set the value of assayType
- setAsText(String) - Method in class net.sourceforge.solexatools.validation.CustomIntegerEditor
- setAttached(boolean) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.SqwFile
-
- setAttribute(String, String) - Method in class net.sourceforge.seqware.common.module.ReturnValue
-
setAttribute.
- setAttributeParent(T) - Method in interface net.sourceforge.seqware.common.model.Attribute
-
Associate this attribute with its parent
- setAttributeParent(Experiment) - Method in class net.sourceforge.seqware.common.model.ExperimentAttribute
-
- setAttributeParent(File) - Method in class net.sourceforge.seqware.common.model.FileAttribute
-
- setAttributeParent(IUS) - Method in class net.sourceforge.seqware.common.model.IUSAttribute
-
- setAttributeParent(Lane) - Method in class net.sourceforge.seqware.common.model.LaneAttribute
-
- setAttributeParent(Processing) - Method in class net.sourceforge.seqware.common.model.ProcessingAttribute
-
- setAttributeParent(Sample) - Method in class net.sourceforge.seqware.common.model.SampleAttribute
-
- setAttributeParent(SampleSearch) - Method in class net.sourceforge.seqware.common.model.SampleSearchAttribute
-
- setAttributeParent(SequencerRunWizardDTO) - Method in class net.sourceforge.seqware.common.model.SequencerRunAttribute
-
- setAttributeParent(Study) - Method in class net.sourceforge.seqware.common.model.StudyAttribute
-
- setAttributeParent(Workflow) - Method in class net.sourceforge.seqware.common.model.WorkflowAttribute
-
- setAttributeParent(WorkflowRun) - Method in class net.sourceforge.seqware.common.model.WorkflowRunAttribute
-
- setAttributes(Map<String, String>) - Method in class net.sourceforge.seqware.common.module.ReturnValue
-
Setter for the field attributes.
- setAttributes(Set<AttributeDto>) - Method in class net.sourceforge.seqware.webservice.dto.LibraryDto
-
Setter for the field attributes.
- setAttributes(Set<AttributeDto>) - Method in class net.sourceforge.seqware.webservice.dto.SampleSearchDto
-
Setter for the field attributes.
- setBarcode(String) - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.SampleInfo
-
Set the value of barcode
- setBarcode(String) - Method in class net.sourceforge.seqware.webservice.dto.IusDto
-
Setter for the field barcode.
- setBaseCaller(String) - Method in class io.seqware.webservice.generated.model.Experiment
-
- setBaseCaller(String) - Method in class io.seqware.webservice.generated.model.SequencerRun
-
- setBaseCaller(String) - Method in class net.sourceforge.seqware.common.model.Experiment
-
Setter for the field baseCaller.
- setBaseCoord(Integer) - Method in class io.seqware.webservice.generated.model.ExperimentSpotDesignReadSpec
-
- setBaseCoord(Integer) - Method in class net.sourceforge.seqware.common.model.ExperimentSpotDesignReadSpec
-
Setter for the field baseCoord.
- setBaseDir(String) - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowInfo
-
Setter for the field baseDir.
- setBaseIniFile(String) - Method in class io.seqware.webservice.generated.model.Workflow
-
- setBaseIniFile(String) - Method in class net.sourceforge.seqware.common.model.Workflow
-
Setter for the field baseIniFile.
- setCell(List<String>) - Method in class net.sourceforge.solexatools.webapp.metamodel.Flexigrid.Cells
-
- setCenterName(String) - Method in class io.seqware.webservice.generated.model.Experiment
-
- setCenterName(String) - Method in class io.seqware.webservice.generated.model.Study
-
- setCenterName(String) - Method in class net.sourceforge.seqware.common.model.Experiment
-
Setter for the field centerName.
- setCenterName(String) - Method in class net.sourceforge.seqware.common.model.Study
-
Setter for the field centerName.
- setCenterProjectName(String) - Method in class io.seqware.webservice.generated.model.Study
-
- setCenterProjectName(String) - Method in class net.sourceforge.seqware.common.model.Study
-
Setter for the field centerProjectName.
- setChildId(Processing) - Method in class io.seqware.webservice.generated.model.ProcessingRelationship
-
- setChildId(Sample) - Method in class io.seqware.webservice.generated.model.SampleRelationship
-
- setChildren(Set<Processing>) - Method in class net.sourceforge.seqware.common.model.Processing
-
Setter for the field children.
- setChildren(Set<Sample>) - Method in class net.sourceforge.seqware.common.model.Sample
-
Setter for the field
children.
- setChildrenUrls(Set<String>) - Method in class net.sourceforge.seqware.webservice.dto.LibraryDto
-
Setter for the field childrenUrls.
- setChildSample(Sample) - Method in class net.sourceforge.seqware.common.model.FileReportRow
-
Setter for the field childSample.
- setChildSample(Sample) - Method in class net.sourceforge.seqware.common.model.SampleReportRow
-
Setter for the field childSample.
- setChildSample(Sample) - Method in class net.sourceforge.seqware.common.model.SequencerRunReportId
-
Setter for the field childSample.
- setChildSample(Sample) - Method in class net.sourceforge.solexatools.webapp.metamodel.StudySampleReportFileLineItem
-
Setter for the field childSample.
- setChildSample(Sample) - Method in class net.sourceforge.solexatools.webapp.metamodel.StudySampleReportLineItem
-
Setter for the field childSample.
- setChildSampleId(Integer) - Method in class io.seqware.webservice.generated.model.FileReport
-
- setChildSampleId(Integer) - Method in class io.seqware.webservice.generated.model.SampleReport
-
- setClassesDir(String) - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowInfo
-
Setter for the field classesDir.
- setClient(Client) - Method in class io.seqware.webservice.generated.client.SeqWareWebserviceClient
-
- setClientNotes(String) - Method in class io.seqware.webservice.generated.model.Invoice
-
- setClientNotes(String) - Method in class net.sourceforge.seqware.common.model.Invoice
-
Setter for the field clientNotes.
- setCmd(String) - Method in class io.seqware.webservice.generated.model.Workflow
-
- setCmd(String) - Method in class io.seqware.webservice.generated.model.WorkflowRun
-
- setCode(String) - Method in class io.seqware.webservice.generated.model.LaneType
-
- setCode(String) - Method in class io.seqware.webservice.generated.model.Organism
-
- setCode(String) - Method in class net.sourceforge.seqware.common.model.Organism
-
Setter for the field code.
- setCode(String) - Method in class net.sourceforge.seqware.webservice.dto.OrganismDto
-
Setter for the field code.
- setColorMatrix(String) - Method in class io.seqware.webservice.generated.model.SequencerRun
-
- setColorMatrix(String) - Method in class net.sourceforge.seqware.common.model.SequencerRun
-
Setter for the field colorMatrix.
- setColorMatrix(String) - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
-
Setter for the field colorMatrix.
- setColorMatrixCode(String) - Method in class io.seqware.webservice.generated.model.SequencerRun
-
- setColorMatrixCode(String) - Method in class net.sourceforge.seqware.common.model.SequencerRun
-
Setter for the field colorMatrixCode.
- setColorMatrixCode(String) - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
-
Setter for the field colorMatrixCode.
- setCommand(String) - Method in class net.sourceforge.seqware.common.model.Workflow
-
Setter for the field command.
- setCommand(String) - Method in class net.sourceforge.seqware.common.model.WorkflowRun
-
Setter for the field command.
- setCommand(String) - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowInfo
-
Setter for the field command.
- setCommand(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.AbstractJob
-
- setCommand(String) - Method in interface net.sourceforge.seqware.pipeline.workflowV2.model.Job
-
set the job command
- setCommand(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.JobBatch
-
- setCommonName(String) - Method in class io.seqware.webservice.generated.model.Sample
-
- setCompleted(int) - Method in class net.sourceforge.solexatools.webapp.metamodel.StudySampleReportLineItem
-
Setter for the field completed.
- setCompute(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Environment
-
- setComputeReq(String) - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowInfo
-
Setter for the field computeReq.
- setConfig(Map<String, String>) - Method in interface net.sourceforge.seqware.pipeline.decider.DeciderInterface
-
Let's you set the config this object should use.
- setConfig(Map<String, String>) - Method in class net.sourceforge.seqware.pipeline.plugin.Plugin
-
Let's you set the config this object should use.
- setConfig(Map<String, String>) - Method in interface net.sourceforge.seqware.pipeline.plugin.PluginInterface
-
Let's you set the config this object should use.
- setConfig(Map<String, String>) - Method in class net.sourceforge.seqware.pipeline.plugins.HelloWorld
-
Let's you set the config this object should use.
- setConfig(Map<String, String>) - Method in class net.sourceforge.seqware.pipeline.plugins.MarkdownPlugin
-
Let's you set the config this object should use.
- setConfig(Map<String, String>) - Method in class net.sourceforge.seqware.pipeline.plugins.WorkflowRunFilesInitialPopulationPlugin
-
Let's you set the config this object should use.
- setConfigPath(String) - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowInfo
-
Setter for the field configPath.
- setConfigs(Map<String, String>) - Method in class net.sourceforge.seqware.pipeline.workflowV2.AbstractWorkflowDataModel
-
set the key-value properties for workflow
- setConfirmEmailAddress(String) - Method in class net.sourceforge.seqware.common.model.RegistrationDTO
-
Setter for the field confirmEmailAddress.
- setConfirmPassword(String) - Method in class net.sourceforge.seqware.common.model.RegistrationDTO
-
Setter for the field confirmPassword.
- setConstructionProtocol(String) - Method in class io.seqware.webservice.generated.model.ExperimentLibraryDesign
-
- setConstructionProtocol(String) - Method in class net.sourceforge.seqware.common.model.ExperimentLibraryDesign
-
Setter for the field constructionProtocol.
- setCountFile(Integer) - Method in class net.sourceforge.seqware.common.model.Sample
-
Setter for the field
countFile.
- setCreated(Date) - Method in class net.sourceforge.seqware.common.model.SampleSearch
-
Setter for the field created.
- setCreateTimestamp(Date) - Method in class net.sourceforge.seqware.common.model.Experiment
-
Setter for the field createTimestamp.
- setCreateTimestamp(Date) - Method in class net.sourceforge.seqware.common.model.Invoice
-
Setter for the field createTimestamp.
- setCreateTimestamp(Date) - Method in class net.sourceforge.seqware.common.model.IUS
-
Setter for the field createTimestamp.
- setCreateTimestamp(Date) - Method in class net.sourceforge.seqware.common.model.Lane
-
Setter for the field createTimestamp.
- setCreateTimestamp(Date) - Method in class net.sourceforge.seqware.common.model.Processing
-
Setter for the field createTimestamp.
- setCreateTimestamp(Date) - Method in class net.sourceforge.seqware.common.model.Registration
-
Setter for the field createTimestamp.
- setCreateTimestamp(Date) - Method in class net.sourceforge.seqware.common.model.Sample
-
Setter for the field
createTimestamp.
- setCreateTimestamp(Date) - Method in class net.sourceforge.seqware.common.model.SequencerRun
-
Setter for the field createTimestamp.
- setCreateTimestamp(Date) - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
-
Setter for the field createTimestamp.
- setCreateTimestamp(Date) - Method in class net.sourceforge.seqware.common.model.ShareStudy
-
Setter for the field createTimestamp.
- setCreateTimestamp(Date) - Method in class net.sourceforge.seqware.common.model.ShareWorkflowRun
-
Setter for the field createTimestamp.
- setCreateTimestamp(Date) - Method in class net.sourceforge.seqware.common.model.Study
-
Setter for the field createTimestamp.
- setCreateTimestamp(Date) - Method in class net.sourceforge.seqware.common.model.Workflow
-
Setter for the field createTimestamp.
- setCreateTimestamp(Date) - Method in class net.sourceforge.seqware.common.model.WorkflowRun
-
Setter for the field createTimestamp.
- setCreateTimeStamp(String) - Method in class net.sourceforge.seqware.webservice.dto.IusDto
-
Setter for the field createTimeStamp.
- setCreateTimeStamp(String) - Method in class net.sourceforge.seqware.webservice.dto.LibraryDto
-
Setter for the field createTimeStamp.
- setCreateTstmp(Date) - Method in class io.seqware.webservice.generated.model.Experiment
-
- setCreateTstmp(Date) - Method in class io.seqware.webservice.generated.model.Invoice
-
- setCreateTstmp(Date) - Method in class io.seqware.webservice.generated.model.Ius
-
- setCreateTstmp(Date) - Method in class io.seqware.webservice.generated.model.Lane
-
- setCreateTstmp(Date) - Method in class io.seqware.webservice.generated.model.Processing
-
- setCreateTstmp(Date) - Method in class io.seqware.webservice.generated.model.Registration
-
- setCreateTstmp(Date) - Method in class io.seqware.webservice.generated.model.Sample
-
- setCreateTstmp(Date) - Method in class io.seqware.webservice.generated.model.SampleSearch
-
- setCreateTstmp(Date) - Method in class io.seqware.webservice.generated.model.SequencerRun
-
- setCreateTstmp(Date) - Method in class io.seqware.webservice.generated.model.ShareExperiment
-
- setCreateTstmp(Date) - Method in class io.seqware.webservice.generated.model.ShareFile
-
- setCreateTstmp(Date) - Method in class io.seqware.webservice.generated.model.ShareLane
-
- setCreateTstmp(Date) - Method in class io.seqware.webservice.generated.model.ShareProcessing
-
- setCreateTstmp(Date) - Method in class io.seqware.webservice.generated.model.ShareSample
-
- setCreateTstmp(Date) - Method in class io.seqware.webservice.generated.model.ShareStudy
-
- setCreateTstmp(Date) - Method in class io.seqware.webservice.generated.model.ShareWorkflowRun
-
- setCreateTstmp(Date) - Method in class io.seqware.webservice.generated.model.Study
-
- setCreateTstmp(Date) - Method in class io.seqware.webservice.generated.model.Workflow
-
- setCreateTstmp(Date) - Method in class io.seqware.webservice.generated.model.WorkflowRun
-
- setCreateTstmp(Date) - Method in class net.sourceforge.seqware.common.model.ShareExperiment
-
Setter for the field createTstmp.
- setCreateTstmp(Date) - Method in class net.sourceforge.seqware.common.model.ShareFile
-
Setter for the field createTstmp.
- setCreateTstmp(Date) - Method in class net.sourceforge.seqware.common.model.ShareLane
-
Setter for the field createTstmp.
- setCreateTstmp(Date) - Method in class net.sourceforge.seqware.common.model.ShareProcessing
-
Setter for the field createTstmp.
- setCreateTstmp(Date) - Method in class net.sourceforge.seqware.common.model.ShareSample
-
Setter for the field createTstmp.
- setCriteria(String) - Method in class net.sourceforge.solexatools.webapp.controller.SearchController
-
Setter for the field criteria.
- setCurrentSelectedFiles(HttpServletRequest, List<File>) - Static method in class net.sourceforge.solexatools.util.LaunchWorkflowUtil
-
setCurrentSelectedFiles.
- setCurrentSelectedNodes(HttpServletRequest, List<String>) - Static method in class net.sourceforge.solexatools.util.LaunchWorkflowUtil
-
setCurrentSelectedNodes.
- setCurrentWorkingDir(String) - Method in class io.seqware.webservice.generated.model.Workflow
-
- setCurrentWorkingDir(String) - Method in class io.seqware.webservice.generated.model.WorkflowRun
-
- setCurrentWorkingDir(String) - Method in class net.sourceforge.seqware.common.model.WorkflowRun
-
Setter for the field currentWorkingDir.
- setCwd(String) - Method in class net.sourceforge.seqware.common.model.Workflow
-
Setter for the field cwd.
- setCycleCoord(Integer) - Method in class io.seqware.webservice.generated.model.ExperimentSpotDesignReadSpec
-
- setCycleCoord(Integer) - Method in class net.sourceforge.seqware.common.model.ExperimentSpotDesignReadSpec
-
Setter for the field cycleCoord.
- setCycleCount(Integer) - Method in class io.seqware.webservice.generated.model.Lane
-
- setCycleCount(Integer) - Method in class io.seqware.webservice.generated.model.SequencerRun
-
- setCycleCount(Integer) - Method in class net.sourceforge.seqware.common.model.SequencerRun
-
Setter for the field cycleCount.
- setCycleCount(Integer) - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
-
Setter for the field cycleCount.
- setCycleDescriptor(String) - Method in class io.seqware.webservice.generated.model.Lane
-
- setCycleDescriptor(String) - Method in class io.seqware.webservice.generated.model.SequencerRun
-
- setCycleDescriptor(String) - Method in class net.sourceforge.seqware.common.model.Lane
-
Setter for the field cycleDescriptor.
- setCycleDescriptor(String) - Method in class net.sourceforge.seqware.common.model.SequencerRun
-
Setter for the field cycleDescriptor.
- setCycleDescriptor(String) - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
-
Setter for the field cycleDescriptor.
- setCycles(String) - Method in class net.sourceforge.seqware.common.model.SequencerRun
-
Setter for the field cycles.
- setCycles(String) - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
-
Setter for the field cycles.
- setCycleSequence(String) - Method in class io.seqware.webservice.generated.model.Lane
-
- setCycleSequence(String) - Method in class io.seqware.webservice.generated.model.SequencerRun
-
- setCycleSequence(String) - Method in class net.sourceforge.seqware.common.model.SequencerRun
-
Setter for the field cycleSequence.
- setCycleSequence(String) - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
-
Setter for the field cycleSequence.
- setDataDecryptionKeyString(String) - Method in class net.sourceforge.seqware.common.util.filetools.ProvisionFilesUtil
-
Sets data decryption key.
- setDataEncryptionKeyString(String) - Method in class net.sourceforge.seqware.common.util.filetools.ProvisionFilesUtil
-
Sets data encryption key.
- setDate(Date) - Method in class net.sourceforge.seqware.common.hibernate.SequencerRunReport.Row
-
- setDate(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.AbstractWorkflowDataModel
-
set the pre-defined date variable
- setDax(String) - Method in class io.seqware.webservice.generated.model.WorkflowRun
-
- setDax(String) - Method in class net.sourceforge.seqware.common.model.WorkflowRun
-
Setter for the field dax.
- setDaxDir(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Environment
-
- setDaysUntilDue(Integer) - Method in class io.seqware.webservice.generated.model.Invoice
-
- setDaysUntilDue(Integer) - Method in class net.sourceforge.seqware.common.model.Invoice
-
Setter for the field daysUntilDue.
- setDb(String) - Method in class io.seqware.webservice.generated.model.ExperimentLink
-
- setDb(String) - Method in class io.seqware.webservice.generated.model.IusLink
-
- setDb(String) - Method in class io.seqware.webservice.generated.model.LaneLink
-
- setDb(String) - Method in class io.seqware.webservice.generated.model.SampleLink
-
- setDb(String) - Method in class io.seqware.webservice.generated.model.StudyLink
-
- setDb(String) - Method in class net.sourceforge.seqware.common.model.ExperimentLink
-
Setter for the field db.
- setDb(String) - Method in class net.sourceforge.seqware.common.model.IUSLink
-
Setter for the field db.
- setDb(String) - Method in class net.sourceforge.seqware.common.model.LaneLink
-
Setter for the field db.
- setDb(String) - Method in class net.sourceforge.seqware.common.model.SampleLink
-
Setter for the field db.
- setDb(String) - Method in class net.sourceforge.seqware.common.model.StudyLink
-
Setter for the field db.
- setDecodeMethod(Integer) - Method in class io.seqware.webservice.generated.model.ExperimentSpotDesign
-
- setDecodeMethod(Integer) - Method in class net.sourceforge.seqware.common.model.ExperimentSpotDesign
-
Setter for the field decodeMethod.
- setDefaultValue(String) - Method in class io.seqware.webservice.generated.model.WorkflowParam
-
- setDefaultValue(String) - Method in class net.sourceforge.seqware.common.model.WorkflowParam
-
Setter for the field defaultValue.
- setDescription(String) - Method in class io.seqware.webservice.generated.model.Expense
-
- setDescription(String) - Method in class io.seqware.webservice.generated.model.Experiment
-
- setDescription(String) - Method in class io.seqware.webservice.generated.model.ExperimentLibraryDesign
-
- setDescription(String) - Method in class io.seqware.webservice.generated.model.File
-
- setDescription(String) - Method in class io.seqware.webservice.generated.model.Ius
-
- setDescription(String) - Method in class io.seqware.webservice.generated.model.Lane
-
- setDescription(String) - Method in class io.seqware.webservice.generated.model.LibrarySelection
-
- setDescription(String) - Method in class io.seqware.webservice.generated.model.LibrarySource
-
- setDescription(String) - Method in class io.seqware.webservice.generated.model.LibraryStrategy
-
- setDescription(String) - Method in class io.seqware.webservice.generated.model.Platform
-
- setDescription(String) - Method in class io.seqware.webservice.generated.model.Processing
-
- setDescription(String) - Method in class io.seqware.webservice.generated.model.ProcessingExperiments
-
- setDescription(String) - Method in class io.seqware.webservice.generated.model.ProcessingIus
-
- setDescription(String) - Method in class io.seqware.webservice.generated.model.ProcessingLanes
-
- setDescription(String) - Method in class io.seqware.webservice.generated.model.ProcessingSamples
-
- setDescription(String) - Method in class io.seqware.webservice.generated.model.ProcessingSequencerRuns
-
- setDescription(String) - Method in class io.seqware.webservice.generated.model.ProcessingStudies
-
- setDescription(String) - Method in class io.seqware.webservice.generated.model.Sample
-
- setDescription(String) - Method in class io.seqware.webservice.generated.model.SequencerRun
-
- setDescription(String) - Method in class io.seqware.webservice.generated.model.Study
-
- setDescription(String) - Method in class io.seqware.webservice.generated.model.StudyType
-
- setDescription(String) - Method in class io.seqware.webservice.generated.model.Workflow
-
- setDescription(String) - Method in class net.sourceforge.seqware.common.model.Expense
-
Setter for the field
description.
- setDescription(String) - Method in class net.sourceforge.seqware.common.model.Experiment
-
Setter for the field description.
- setDescription(String) - Method in class net.sourceforge.seqware.common.model.ExperimentLibraryDesign
-
Setter for the field description.
- setDescription(String) - Method in class net.sourceforge.seqware.common.model.File
-
Setter for the field description.
- setDescription(String) - Method in class net.sourceforge.seqware.common.model.IUS
-
Setter for the field description.
- setDescription(String) - Method in class net.sourceforge.seqware.common.model.Lane
-
Setter for the field description.
- setDescription(String) - Method in class net.sourceforge.seqware.common.model.LibrarySelection
-
Setter for the field description.
- setDescription(String) - Method in class net.sourceforge.seqware.common.model.LibrarySource
-
Setter for the field description.
- setDescription(String) - Method in class net.sourceforge.seqware.common.model.LibraryStrategy
-
Setter for the field description.
- setDescription(String) - Method in class net.sourceforge.seqware.common.model.Platform
-
Setter for the field description.
- setDescription(String) - Method in class net.sourceforge.seqware.common.model.Processing
-
Setter for the field description.
- setDescription(String) - Method in class net.sourceforge.seqware.common.model.ProcessingExperiments
-
Setter for the field description.
- setDescription(String) - Method in class net.sourceforge.seqware.common.model.ProcessingIus
-
Setter for the field description.
- setDescription(String) - Method in class net.sourceforge.seqware.common.model.ProcessingLanes
-
Setter for the field description.
- setDescription(String) - Method in class net.sourceforge.seqware.common.model.ProcessingSamples
-
Setter for the field description.
- setDescription(String) - Method in class net.sourceforge.seqware.common.model.ProcessingSequencerRuns
-
Setter for the field description.
- setDescription(String) - Method in class net.sourceforge.seqware.common.model.ProcessingStudies
-
Setter for the field description.
- setDescription(String) - Method in class net.sourceforge.seqware.common.model.Sample
-
Setter for the field
description.
- setDescription(String) - Method in class net.sourceforge.seqware.common.model.SequencerRun
-
Setter for the field description.
- setDescription(String) - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
-
Setter for the field description.
- setDescription(String) - Method in class net.sourceforge.seqware.common.model.Study
-
Setter for the field description.
- setDescription(String) - Method in class net.sourceforge.seqware.common.model.StudyType
-
Setter for the field description.
- setDescription(String) - Method in class net.sourceforge.seqware.common.model.Workflow
-
Setter for the field description.
- setDescription(String) - Method in class net.sourceforge.seqware.common.module.FileMetadata
-
- setDescription(String) - Method in class net.sourceforge.seqware.common.module.ReturnValue
-
Setter for the field description.
- setDescription(String) - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowInfo
-
Setter for the field description.
- setDescription(String) - Method in class net.sourceforge.seqware.webservice.dto.FileDto
-
Setter for the field description.
- setDescription(String) - Method in class net.sourceforge.seqware.webservice.dto.LibraryDto
-
Setter for the field description.
- setDeveloperMl(boolean) - Method in class io.seqware.webservice.generated.model.Registration
-
- setDisplay(Boolean) - Method in class io.seqware.webservice.generated.model.WorkflowParam
-
- setDisplay(Boolean) - Method in class net.sourceforge.seqware.common.model.WorkflowParam
-
Setter for the field display.
- setDisplay(String) - Method in class net.sourceforge.solexatools.webapp.metamodel.Flexigrid.ColumnModel
-
- setDisplayName(String) - Method in class io.seqware.webservice.generated.model.FileType
-
- setDisplayName(String) - Method in class io.seqware.webservice.generated.model.WorkflowParam
-
- setDisplayName(String) - Method in class io.seqware.webservice.generated.model.WorkflowParamValue
-
- setDisplayName(String) - Method in class net.sourceforge.seqware.common.model.FileType
-
Setter for the field displayName.
- setDisplayName(String) - Method in class net.sourceforge.seqware.common.model.WorkflowParam
-
Setter for the field displayName.
- setDisplayName(String) - Method in class net.sourceforge.seqware.common.model.WorkflowParamValue
-
Setter for the field displayName.
- setDisplayName(String) - Method in class net.sourceforge.solexatools.util.SummaryLine
-
Setter for the field displayName.
- setDisplayValue(String) - Method in class net.sourceforge.seqware.common.model.WorkflowParam
-
Setter for the field displayValue.
- setDomainObject(Registration) - Method in class net.sourceforge.seqware.common.model.RegistrationDTO
-
Setter for the field domainObject.
- setDomainObject(Registration) - Method in class net.sourceforge.seqware.common.model.SequencerRunWizardDTO
-
Setter for the field domainObject.
- setEarliestDate(Date) - Method in class net.sourceforge.seqware.common.hibernate.WorkflowRunReport
-
Set the value of earliestDate.
- setEmail(String) - Method in class io.seqware.webservice.generated.model.Registration
-
- setEmail(String) - Method in class net.sourceforge.seqware.webservice.dto.OwnerDto
-
Setter for the field email.
- setEmailAddress(String) - Method in class net.sourceforge.seqware.common.model.Registration
-
Setter for the field emailAddress.
- setEnd(String) - Method in class net.sourceforge.seqware.common.model.UploadSequence
-
Setter for the field end.
- setEndDate(Date) - Method in class io.seqware.webservice.generated.model.Invoice
-
- setEndDate(Date) - Method in class net.sourceforge.seqware.common.model.Invoice
-
Setter for the field endDate.
- setEndPage(String) - Method in class net.sourceforge.solexatools.util.PageInfo
-
Setter for the field endPage.
- setEntityUrl(String) - Method in class net.sourceforge.seqware.webservice.dto.AttributeDto
-
Setter for the field entityUrl.
- setErrorCount(Integer) - Method in class net.sourceforge.seqware.common.model.SequencerRun
-
Setter for the field errorCount.
- setExecutionEnv(Environment.ExecutionEnvironment) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Environment
-
set the execution environment
- setExistingType(StudyType) - Method in class io.seqware.webservice.generated.model.Study
-
- setExistingType(StudyType) - Method in class net.sourceforge.seqware.common.model.Study
-
Setter for the field existingType.
- setExistingTypeInt(Integer) - Method in class net.sourceforge.seqware.common.model.Study
-
Setter for the field existingTypeInt.
- setExitCode(int) - Method in exception net.sourceforge.seqware.common.err.OldSeqwareException
-
Setter for the field exitCode.
- setExitStatus(Integer) - Method in class io.seqware.webservice.generated.model.Processing
-
- setExitStatus(Integer) - Method in class net.sourceforge.seqware.common.model.Processing
-
Setter for the field exitStatus.
- setExitStatus(int) - Method in class net.sourceforge.seqware.common.module.ReturnValue
-
Setter for the field exitStatus.
- setExpectedBasecall(String) - Method in class io.seqware.webservice.generated.model.ExperimentSpotDesignReadSpec
-
- setExpectedBaseCall(String) - Method in class net.sourceforge.seqware.common.model.ExperimentSpotDesignReadSpec
-
Setter for the field expectedBaseCall.
- setExpectedNumberReads(BigInteger) - Method in class io.seqware.webservice.generated.model.Experiment
-
- setExpectedNumberReads(Integer) - Method in class io.seqware.webservice.generated.model.Sample
-
- setExpectedNumberReads(Long) - Method in class net.sourceforge.seqware.common.model.Experiment
-
Setter for the field expectedNumberReads.
- setExpectedNumberRuns(Integer) - Method in class io.seqware.webservice.generated.model.Experiment
-
- setExpectedNumberRuns(Integer) - Method in class io.seqware.webservice.generated.model.Sample
-
- setExpectedNumberRuns(Integer) - Method in class net.sourceforge.seqware.common.model.Experiment
-
Setter for the field expectedNumberRuns.
- setExpectedNumberSpots(BigInteger) - Method in class io.seqware.webservice.generated.model.Experiment
-
- setExpectedNumberSpots(Integer) - Method in class io.seqware.webservice.generated.model.Sample
-
- setExpectedNumberSpots(Long) - Method in class net.sourceforge.seqware.common.model.Experiment
-
Setter for the field expectedNumberSpots.
- setExpectedNumReads(Integer) - Method in class net.sourceforge.seqware.common.model.Sample
-
Setter for the field
expectedNumReads.
- setExpectedNumRuns(Integer) - Method in class net.sourceforge.seqware.common.model.Sample
-
Setter for the field
expectedNumRuns.
- setExpectedNumSpots(Integer) - Method in class net.sourceforge.seqware.common.model.Sample
-
Setter for the field
expectedNumSpots.
- setExpenseAttributeCollection(Collection<ExpenseAttribute>) - Method in class io.seqware.webservice.generated.model.Expense
-
- setExpenseAttributeId(Integer) - Method in class io.seqware.webservice.generated.model.ExpenseAttribute
-
- setExpenseCollection(Collection<Expense>) - Method in class io.seqware.webservice.generated.model.Invoice
-
- setExpenseFinishedTstmp(Date) - Method in class io.seqware.webservice.generated.model.Expense
-
- setExpenseId(Integer) - Method in class io.seqware.webservice.generated.model.Expense
-
- setExpenseId(Expense) - Method in class io.seqware.webservice.generated.model.ExpenseAttribute
-
- setExpenseId(Integer) - Method in class net.sourceforge.seqware.common.model.Expense
-
Setter for the field
expenseId.
- setExpenses(Set<Expense>) - Method in class net.sourceforge.seqware.common.model.Invoice
-
Setter for the field expenses.
- setExpenseType(String) - Method in class io.seqware.webservice.generated.model.Expense
-
- setExpenseType(String) - Method in class net.sourceforge.seqware.common.model.Expense
-
Setter for the field
expenseType.
- setExperiment(Experiment) - Method in class net.sourceforge.seqware.common.model.ExperimentAttribute
-
Setter for the field experiment.
- setExperiment(Experiment) - Method in class net.sourceforge.seqware.common.model.ExperimentLink
-
Setter for the field experiment.
- setExperiment(Experiment) - Method in class net.sourceforge.seqware.common.model.FileReportRow
-
Setter for the field experiment.
- setExperiment(Experiment) - Method in class net.sourceforge.seqware.common.model.ProcessingExperiments
-
Setter for the field experiment.
- setExperiment(Experiment) - Method in class net.sourceforge.seqware.common.model.Sample
-
Setter for the field
experiment.
- setExperiment(Experiment) - Method in class net.sourceforge.seqware.common.model.ShareExperiment
-
Setter for the field experiment.
- setExperiment(Experiment, HttpServletRequest) - Static method in class net.sourceforge.solexatools.util.SetNodeIdInSession
-
setExperiment.
- setExperimentAttributeCollection(Collection<ExperimentAttribute>) - Method in class io.seqware.webservice.generated.model.Experiment
-
- setExperimentAttributeId(Integer) - Method in class io.seqware.webservice.generated.model.ExperimentAttribute
-
- setExperimentAttributeId(int) - Method in class net.sourceforge.seqware.common.model.ExperimentAttribute
-
Setter for the field experimentAttributeId.
- setExperimentAttributes(Set<ExperimentAttribute>) - Method in class net.sourceforge.seqware.common.model.Experiment
-
Setter for the field experimentAttributes.
- setExperimentAttributes(Set<TagValueUnit>) - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.RunInfo
-
Set the value of experimentAttributes
- setExperimentCollection(Collection<Experiment>) - Method in class io.seqware.webservice.generated.model.ExperimentLibraryDesign
-
- setExperimentCollection(Collection<Experiment>) - Method in class io.seqware.webservice.generated.model.ExperimentSpotDesign
-
- setExperimentCollection(Collection<Experiment>) - Method in class io.seqware.webservice.generated.model.Platform
-
- setExperimentCollection(Collection<Experiment>) - Method in class io.seqware.webservice.generated.model.Registration
-
- setExperimentCollection(Collection<Experiment>) - Method in class io.seqware.webservice.generated.model.Study
-
- setExperimentDAO(ExperimentDAO) - Method in interface net.sourceforge.seqware.common.business.ExperimentService
-
setExperimentDAO.
- setExperimentDAO(ExperimentDAO) - Method in class net.sourceforge.seqware.common.business.impl.ExperimentServiceImpl
-
setExperimentDAO.
- setExperimentDAO(ExperimentDAO) - Method in class net.sourceforge.seqware.common.business.impl.FileUploadServiceImpl
-
Setter for the field experimentDAO.
- setExperimentDescription(String) - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.RunInfo
-
Set the value of experimentDescription
- setExperimentId(Integer) - Method in class io.seqware.webservice.generated.model.Experiment
-
- setExperimentId(Experiment) - Method in class io.seqware.webservice.generated.model.ExperimentAttribute
-
- setExperimentId(Experiment) - Method in class io.seqware.webservice.generated.model.ExperimentLink
-
- setExperimentId(Integer) - Method in class io.seqware.webservice.generated.model.FileReport
-
- setExperimentId(Experiment) - Method in class io.seqware.webservice.generated.model.ProcessingExperiments
-
- setExperimentId(Experiment) - Method in class io.seqware.webservice.generated.model.Sample
-
- setExperimentId(Experiment) - Method in class io.seqware.webservice.generated.model.ShareExperiment
-
- setExperimentId(Integer) - Method in class net.sourceforge.seqware.common.model.Experiment
-
Setter for the field experimentId.
- setExperimentLibraryDesign(ExperimentLibraryDesign) - Method in class net.sourceforge.seqware.common.model.Experiment
-
Setter for the field experimentLibraryDesign.
- setExperimentLibraryDesignCollection(Collection<ExperimentLibraryDesign>) - Method in class io.seqware.webservice.generated.model.LibrarySelection
-
- setExperimentLibraryDesignCollection(Collection<ExperimentLibraryDesign>) - Method in class io.seqware.webservice.generated.model.LibrarySource
-
- setExperimentLibraryDesignCollection(Collection<ExperimentLibraryDesign>) - Method in class io.seqware.webservice.generated.model.LibraryStrategy
-
- setExperimentLibraryDesignDAO(ExperimentLibraryDesignDAO) - Method in interface net.sourceforge.seqware.common.business.ExperimentLibraryDesignService
-
setExperimentLibraryDesignDAO.
- setExperimentLibraryDesignDAO(ExperimentLibraryDesignDAO) - Method in class net.sourceforge.seqware.common.business.impl.ExperimentLibraryDesignServiceImpl
-
setExperimentLibraryDesignDAO.
- setExperimentLibraryDesignId(ExperimentLibraryDesign) - Method in class io.seqware.webservice.generated.model.Experiment
-
- setExperimentLibraryDesignId(Integer) - Method in class io.seqware.webservice.generated.model.ExperimentLibraryDesign
-
- setExperimentLibraryDesignId(Integer) - Method in class net.sourceforge.seqware.common.model.ExperimentLibraryDesign
-
Setter for the field experimentLibraryDesignId.
- setExperimentLibraryDesignService(ExperimentLibraryDesignService) - Method in class net.sourceforge.seqware.common.ContextImpl
-
- setExperimentLibraryDesignService(ExperimentLibraryDesignService) - Method in class net.sourceforge.solexatools.webapp.controller.ExperimentController
-
Setter for the field experimentLibraryDesignService.
- setExperimentLinkCollection(Collection<ExperimentLink>) - Method in class io.seqware.webservice.generated.model.Experiment
-
- setExperimentLinkId(Integer) - Method in class io.seqware.webservice.generated.model.ExperimentLink
-
- setExperimentLinkId(int) - Method in class net.sourceforge.seqware.common.model.ExperimentLink
-
Setter for the field experimentLinkId.
- setExperimentLinks(Set<ExperimentLink>) - Method in class net.sourceforge.seqware.common.model.Experiment
-
Setter for the field experimentLinks.
- setExperimentName(String) - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.RunInfo
-
Set the value of experimentName
- setExperiments(Set<Experiment>) - Method in class net.sourceforge.seqware.common.model.Processing
-
Setter for the field experiments.
- setExperiments(SortedSet<Experiment>) - Method in class net.sourceforge.seqware.common.model.Study
-
Setter for the field experiments.
- setExperimentService(ExperimentService) - Method in class net.sourceforge.seqware.common.ContextImpl
-
Setter for the field experimentService.
- setExperimentService(ExperimentService) - Method in class net.sourceforge.solexatools.validation.ExperimentValidator
-
Setter for the field experimentService.
- setExperimentService(ExperimentService) - Method in class net.sourceforge.solexatools.webapp.controller.BulkDownloadListDetailsController
-
Setter for the field experimentService.
- setExperimentService(ExperimentService) - Method in class net.sourceforge.solexatools.webapp.controller.DownloadFileListController
-
Setter for the field experimentService.
- setExperimentService(ExperimentService) - Method in class net.sourceforge.solexatools.webapp.controller.EntityController
-
Setter for the field experimentService.
- setExperimentService(ExperimentService) - Method in class net.sourceforge.solexatools.webapp.controller.ExperimentController
-
Setter for the field experimentService.
- setExperimentService(ExperimentService) - Method in class net.sourceforge.solexatools.webapp.controller.ExperimentSetupController
-
Setter for the field experimentService.
- setExperimentService(ExperimentService) - Method in class net.sourceforge.solexatools.webapp.controller.LaunchWorkflowListDetailsController
-
Setter for the field experimentService.
- setExperimentService(ExperimentService) - Method in class net.sourceforge.solexatools.webapp.controller.SampleController
-
Setter for the field experimentService.
- setExperimentService(ExperimentService) - Method in class net.sourceforge.solexatools.webapp.controller.SampleSetupController
-
Setter for the field experimentService.
- setExperimentService(ExperimentService) - Method in class net.sourceforge.solexatools.webapp.controller.SaveOpenNodeController
-
Setter for the field experimentService.
- setExperimentService(ExperimentService) - Method in class net.sourceforge.solexatools.webapp.controller.SearchResultsListController
-
Setter for the field experimentService.
- setExperimentService(ExperimentService) - Method in class net.sourceforge.solexatools.webapp.controller.SelectInputListController
-
Setter for the field experimentService.
- setExperimentService(ExperimentService) - Method in class net.sourceforge.solexatools.webapp.controller.StudyListDetailsController
-
Setter for the field experimentService.
- setExperimentService(ExperimentService) - Method in class net.sourceforge.solexatools.webapp.controller.StudyListDetailsFlatController
-
Setter for the field experimentService.
- setExperimentService(ExperimentService) - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileController
-
Setter for the field experimentService.
- setExperimentService(ExperimentService) - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileSetupController
-
Setter for the field experimentService.
- setExperimentSpotDesign(ExperimentSpotDesign) - Method in class net.sourceforge.seqware.common.model.Experiment
-
Setter for the field experimentSpotDesign.
- setExperimentSpotDesign(ExperimentSpotDesign) - Method in class net.sourceforge.seqware.common.model.ExperimentSpotDesignReadSpec
-
Setter for the field experimentSpotDesign.
- setExperimentSpotDesignDAO(ExperimentSpotDesignDAO) - Method in interface net.sourceforge.seqware.common.business.ExperimentSpotDesignService
-
setExperimentSpotDesignDAO.
- setExperimentSpotDesignDAO(ExperimentSpotDesignDAO) - Method in class net.sourceforge.seqware.common.business.impl.ExperimentSpotDesignServiceImpl
-
setExperimentSpotDesignDAO.
- setExperimentSpotDesignId(ExperimentSpotDesign) - Method in class io.seqware.webservice.generated.model.Experiment
-
- setExperimentSpotDesignId(Integer) - Method in class io.seqware.webservice.generated.model.ExperimentSpotDesign
-
- setExperimentSpotDesignId(ExperimentSpotDesign) - Method in class io.seqware.webservice.generated.model.ExperimentSpotDesignReadSpec
-
- setExperimentSpotDesignId(Integer) - Method in class net.sourceforge.seqware.common.model.ExperimentSpotDesign
-
Setter for the field experimentSpotDesignId.
- setExperimentSpotDesignReadSpecCollection(Collection<ExperimentSpotDesignReadSpec>) - Method in class io.seqware.webservice.generated.model.ExperimentSpotDesign
-
- setExperimentSpotDesignReadSpecDAO(ExperimentSpotDesignReadSpecDAO) - Method in interface net.sourceforge.seqware.common.business.ExperimentSpotDesignReadSpecService
-
setExperimentSpotDesignReadSpecDAO.
- setExperimentSpotDesignReadSpecDAO(ExperimentSpotDesignReadSpecDAO) - Method in class net.sourceforge.seqware.common.business.impl.ExperimentSpotDesignReadSpecServiceImpl
-
setExperimentSpotDesignReadSpecDAO.
- setExperimentSpotDesignReadSpecId(Integer) - Method in class io.seqware.webservice.generated.model.ExperimentSpotDesignReadSpec
-
- setExperimentSpotDesignReadSpecId(Integer) - Method in class net.sourceforge.seqware.common.model.ExperimentSpotDesignReadSpec
-
Setter for the field experimentSpotDesignReadSpecId.
- setExperimentSpotDesignReadSpecService(ExperimentSpotDesignReadSpecService) - Method in class net.sourceforge.seqware.common.ContextImpl
-
- setExperimentSpotDesignReadSpecService(ExperimentSpotDesignReadSpecService) - Method in class net.sourceforge.solexatools.webapp.controller.ExperimentController
-
Setter for the field experimentSpotDesignReadSpecService.
- setExperimentSpotDesignService(ExperimentSpotDesignService) - Method in class net.sourceforge.seqware.common.ContextImpl
-
- setExperimentSpotDesignService(ExperimentSpotDesignService) - Method in class net.sourceforge.solexatools.webapp.controller.ExperimentController
-
Setter for the field experimentSpotDesignService.
- setExperimentSwas(Set<String>) - Method in class net.sourceforge.seqware.common.business.impl.ValidationReportServiceImpl.ReportEntry
-
- setExpLibDesignDesc(String) - Method in class net.sourceforge.seqware.common.model.Experiment
-
Setter for the field expLibDesignDesc.
- setExpLibDesignName(String) - Method in class net.sourceforge.seqware.common.model.Experiment
-
Setter for the field expLibDesignName.
- setExpLibDesignProtocol(String) - Method in class net.sourceforge.seqware.common.model.Experiment
-
Setter for the field expLibDesignProtocol.
- setExpLibDesignSelection(Integer) - Method in class net.sourceforge.seqware.common.model.Experiment
-
Setter for the field expLibDesignSelection.
- setExpLibDesignSource(Integer) - Method in class net.sourceforge.seqware.common.model.Experiment
-
Setter for the field expLibDesignSource.
- setExpLibDesignStrategy(Integer) - Method in class net.sourceforge.seqware.common.model.Experiment
-
Setter for the field expLibDesignStrategy.
- setExpSpotDesignAdapterSpec(String) - Method in class net.sourceforge.seqware.common.model.Experiment
-
Setter for the field expSpotDesignAdapterSpec.
- setExpSpotDesignReadsPerSpot(Integer) - Method in class net.sourceforge.seqware.common.model.Experiment
-
Setter for the field expSpotDesignReadsPerSpot.
- setExpSpotDesignTagSpec(String) - Method in class net.sourceforge.seqware.common.model.Experiment
-
Setter for the field expSpotDesignTagSpec.
- setExtension(String) - Method in class io.seqware.webservice.generated.model.FileType
-
- setExtension(String) - Method in class net.sourceforge.seqware.common.model.FileType
-
Setter for the field extension.
- setExternalId(String) - Method in class io.seqware.webservice.generated.model.Invoice
-
- setExternalId(String) - Method in class net.sourceforge.seqware.common.model.Invoice
-
Setter for the field externalId.
- setFailed(int) - Method in class net.sourceforge.solexatools.webapp.metamodel.StudySampleReportLineItem
-
Setter for the field failed.
- setFile(MultipartFile) - Method in class net.sourceforge.seqware.common.business.UploadFile
-
Setter for the field file.
- setFile(File) - Method in class net.sourceforge.seqware.common.model.FileAttribute
-
Setter for the field file.
- setFile(File) - Method in class net.sourceforge.seqware.common.model.FileReportRow
-
Setter for the field file.
- setFile(File) - Method in class net.sourceforge.seqware.common.model.ShareFile
-
Setter for the field file.
- setFile(File) - Method in class net.sourceforge.solexatools.webapp.metamodel.StudySampleReportFileLineItem
-
Setter for the field file.
- setFileAttributeCollection(Collection<FileAttribute>) - Method in class io.seqware.webservice.generated.model.File
-
- setFileAttributeId(Integer) - Method in class io.seqware.webservice.generated.model.FileAttribute
-
- setFileAttributeId(Integer) - Method in class net.sourceforge.seqware.common.model.FileAttribute
-
Setter for the field fileAttributeId.
- setFileAttributes(Set<FileAttribute>) - Method in class net.sourceforge.seqware.common.model.File
-
Setter for the field fileAttributes.
- setFileCollection(Collection<File>) - Method in class io.seqware.webservice.generated.model.FileType
-
- setFileCollection(Collection<File>) - Method in class io.seqware.webservice.generated.model.Registration
-
- setFileCollection(Collection<File>) - Method in class io.seqware.webservice.generated.model.WorkflowRun
-
- setFileDAO(FileDAO) - Method in interface net.sourceforge.seqware.common.business.FileService
-
setFileDAO.
- setFileDAO(FileDAO) - Method in class net.sourceforge.seqware.common.business.impl.ExperimentServiceImpl
-
Sets a private member variable with an instance of an implementation of
FileDAO.
- setFileDAO(FileDAO) - Method in class net.sourceforge.seqware.common.business.impl.FileServiceImpl
-
setFileDAO.
- setFileDAO(FileDAO) - Method in class net.sourceforge.seqware.common.business.impl.FileUploadServiceImpl
-
Sets a private member variable with an instance of an implementation of
FileDAO.
- setFileDAO(FileDAO) - Method in class net.sourceforge.seqware.common.business.impl.IUSServiceImpl
-
Setter for the field fileDAO.
- setFileDAO(FileDAO) - Method in class net.sourceforge.seqware.common.business.impl.LaneServiceImpl
-
Sets a private member variable with an instance of an implementation of
FileDAO.
- setFileDAO(FileDAO) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingServiceImpl
-
Sets a private member variable with an instance of an implementation of
FileDAO.
- setFileDAO(FileDAO) - Method in class net.sourceforge.seqware.common.business.impl.SampleServiceImpl
-
Sets a private member variable with an instance of an implementation of
FileDAO.
- setFileDAO(FileDAO) - Method in class net.sourceforge.seqware.common.business.impl.SequencerRunServiceImpl
-
Sets a private member variable with an instance of an implementation of
FileDAO.
- setFileDAO(FileDAO) - Method in class net.sourceforge.seqware.common.business.impl.StudyServiceImpl
-
Sets a private member variable with an instance of an implementation of
FileDAO.
- setFileDAO(FileDAO) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowRunServiceImpl
-
Sets a private member variable with an instance of an implementation of
FileDAO.
- setFileForSequrncerRun(Processing, HttpServletRequest) - Static method in class net.sourceforge.solexatools.util.SetNodeIdInSession
-
setFileForSequrncerRun.
- setFileForStudy(Processing, HttpServletRequest) - Static method in class net.sourceforge.solexatools.util.SetNodeIdInSession
-
setFileForStudy.
- setFileForWorkflowRun(Processing, HttpServletRequest) - Static method in class net.sourceforge.solexatools.util.SetNodeIdInSession
-
setFileForWorkflowRun.
- setFileForWorkflowRunRunning(Processing, HttpServletRequest) - Static method in class net.sourceforge.solexatools.util.SetNodeIdInSession
-
setFileForWorkflowRunRunning.
- setFileId(Integer) - Method in class io.seqware.webservice.generated.model.File
-
- setFileId(File) - Method in class io.seqware.webservice.generated.model.FileAttribute
-
- setFileId(Integer) - Method in class io.seqware.webservice.generated.model.FileReport
-
- setFileId(File) - Method in class io.seqware.webservice.generated.model.ProcessingFiles
-
- setFileId(File) - Method in class io.seqware.webservice.generated.model.ShareFile
-
- setFileId(Integer) - Method in class net.sourceforge.seqware.common.model.File
-
Setter for the field fileId.
- setFileMetaType(String) - Method in class io.seqware.webservice.generated.model.WorkflowParam
-
- setFileMetaType(String) - Method in class net.sourceforge.seqware.common.model.WorkflowParam
-
Setter for the field fileMetaType.
- setFileMetaType(String) - Method in class net.sourceforge.solexatools.util.SummaryLine
-
Setter for the field fileMetaType.
- setFilename(String) - Method in class net.sourceforge.seqware.common.business.impl.ValidationReportServiceImpl.ReportEntry
-
- setFilename(String) - Method in class net.sourceforge.seqware.pipeline.plugins.filelinker.FileLinkerLine
-
- setFileOne(MultipartFile) - Method in class net.sourceforge.seqware.common.model.UploadSequence
-
Setter for the field fileOne.
- setFilePath(String) - Method in class io.seqware.webservice.generated.model.File
-
- setFilePath(String) - Method in class io.seqware.webservice.generated.model.SequencerRun
-
- setFilePath(String) - Method in class net.sourceforge.seqware.common.model.File
-
Setter for the field filePath.
- setFilePath(String) - Method in class net.sourceforge.seqware.common.model.Processing
-
Setter for the field filePath.
- setFilePath(String) - Method in class net.sourceforge.seqware.common.model.SequencerRun
-
Setter for the field filePath.
- setFilePath(String) - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
-
Setter for the field filePath.
- setFilePath(String) - Method in class net.sourceforge.seqware.common.module.FileMetadata
-
- setFilePath(File) - Method in class net.sourceforge.seqware.common.module.FileMetadata
-
- setFilePath(String) - Method in class net.sourceforge.seqware.webservice.dto.FileDto
-
Setter for the field filePath.
- setFileReportDAO(FileReportDAO) - Method in class net.sourceforge.seqware.common.business.impl.FileReportServiceImpl
-
Setter for the field fileReportDAO.
- setFileReportService(FileReportService) - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunReportTableController
-
Setter for the field fileReportService.
- setFileReportService(FileReportService) - Method in class net.sourceforge.solexatools.webapp.controller.StudyReportBoxController
-
Setter for the field fileReportService.
- setFileReportService(FileReportService) - Method in class net.sourceforge.solexatools.webapp.controller.StudyReportTableController
-
Setter for the field fileReportService.
- setFiles(Set<File>) - Method in class net.sourceforge.seqware.common.model.Processing
-
Setter for the field files.
- setFiles(List<File>) - Method in class net.sourceforge.seqware.common.model.WorkflowParam
-
Setter for the field files.
- setFiles(ArrayList<FileMetadata>) - Method in class net.sourceforge.seqware.common.module.ReturnValue
-
Setter for the field files.
- setFiles(List<File>) - Method in class net.sourceforge.solexatools.util.SummaryLine
-
Setter for the field files.
- setFiles_url(String) - Method in class net.sourceforge.seqware.webservice.dto.IusDto
-
Setter for the field files_url.
- setFilesArray(ArrayList<File>) - Method in class net.sourceforge.seqware.pipeline.bundle.Bundle
-
Setter for the field filesArray.
- setFileService(FileService) - Method in class net.sourceforge.seqware.common.ContextImpl
-
Setter for the field fileService.
- setFileService(FileService) - Method in class net.sourceforge.solexatools.validation.UploadFileValidator
-
Setter for the field fileService.
- setFileService(FileService) - Method in class net.sourceforge.solexatools.validation.UploadSequenceValidator
-
Setter for the field fileService.
- setFileService(FileService) - Method in class net.sourceforge.solexatools.webapp.controller.BulkDownloaderController
-
Setter for the field fileService.
- setFileService(FileService) - Method in class net.sourceforge.solexatools.webapp.controller.BulkDownloadListDetailsController
-
Setter for the field fileService.
- setFileService(FileService) - Method in class net.sourceforge.solexatools.webapp.controller.DownloaderController
-
Setter for the field fileService.
- setFileService(FileService) - Method in class net.sourceforge.solexatools.webapp.controller.DownloadFileListController
-
Setter for the field fileService.
- setFileService(FileService) - Method in class net.sourceforge.solexatools.webapp.controller.EntityController
-
Setter for the field fileService.
- setFileService(FileService) - Method in class net.sourceforge.solexatools.webapp.controller.FileController
-
Setter for the field fileService.
- setFileService(FileService) - Method in class net.sourceforge.solexatools.webapp.controller.FileSetupController
-
Setter for the field fileService.
- setFileService(FileService) - Method in class net.sourceforge.solexatools.webapp.controller.LaunchWorkflowListDetailsController
-
Setter for the field fileService.
- setFileService(FileService) - Method in class net.sourceforge.solexatools.webapp.controller.LoadIndexPageController
-
Setter for the field fileService.
- setFileService(FileService) - Method in class net.sourceforge.solexatools.webapp.controller.SaveOpenNodeController
-
Setter for the field fileService.
- setFileService(FileService) - Method in class net.sourceforge.solexatools.webapp.controller.SearchResultsListController
-
Setter for the field fileService.
- setFileService(FileService) - Method in class net.sourceforge.solexatools.webapp.controller.SelectInputListController
-
Setter for the field fileService.
- setFileService(FileService) - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileController
-
Setter for the field fileService.
- setFileService(FileService) - Method in class net.sourceforge.solexatools.webapp.controller.UploadSequenceController
-
Setter for the field fileService.
- setFileStatus(String) - Method in class net.sourceforge.seqware.pipeline.plugins.filelinker.FileLinkerLine
-
- setFileSwa(String) - Method in class net.sourceforge.seqware.common.business.impl.ValidationReportServiceImpl.ReportEntry
-
- setFileTwo(MultipartFile) - Method in class net.sourceforge.seqware.common.model.UploadSequence
-
Setter for the field fileTwo.
- setFileTwoURL(String) - Method in class net.sourceforge.seqware.common.model.UploadSequence
-
Setter for the field fileTwoURL.
- setFileType(FileType) - Method in class net.sourceforge.seqware.common.business.UploadFile
-
Setter for the field fileType.
- setFileType(FileType) - Method in class net.sourceforge.seqware.common.model.File
-
Setter for the field fileType.
- setFileType(FileType) - Method in class net.sourceforge.seqware.common.model.UploadSequence
-
Setter for the field fileType.
- setFileTypeDAO(FileTypeDAO) - Method in interface net.sourceforge.seqware.common.business.FileTypeService
-
setFileTypeDAO.
- setFileTypeDAO(FileTypeDAO) - Method in class net.sourceforge.seqware.common.business.impl.FileTypeServiceImpl
-
setFileTypeDAO.
- setFileTypeDAO(FileTypeDAO) - Method in class net.sourceforge.seqware.common.business.impl.FileUploadServiceImpl
-
Setter for the field fileTypeDAO.
- setFileTypeId(FileType) - Method in class io.seqware.webservice.generated.model.File
-
- setFileTypeId(Integer) - Method in class io.seqware.webservice.generated.model.FileType
-
- setFileTypeId(Integer) - Method in class net.sourceforge.seqware.common.business.UploadFile
-
Setter for the field fileTypeId.
- setFileTypeId(Integer) - Method in class net.sourceforge.seqware.common.model.FileType
-
Setter for the field fileTypeId.
- setFileTypeId(Integer) - Method in class net.sourceforge.seqware.common.model.UploadSequence
-
Setter for the field fileTypeId.
- setFileTypeService(FileTypeService) - Method in class net.sourceforge.solexatools.validation.UploadFileValidator
-
Setter for the field fileTypeService.
- setFileTypeService(FileTypeService) - Method in class net.sourceforge.solexatools.validation.UploadSequenceValidator
-
Setter for the field fileTypeService.
- setFileTypeService(FileTypeService) - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileController
-
Setter for the field fileTypeService.
- setFileTypeService(FileTypeService) - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileSetupController
-
Setter for the field fileTypeService.
- setFileTypeService(FileTypeService) - Method in class net.sourceforge.solexatools.webapp.controller.UploadSequenceController
-
Setter for the field fileTypeService.
- setFileTypeService(FileTypeService) - Method in class net.sourceforge.solexatools.webapp.controller.UploadSequenceSetupController
-
Setter for the field fileTypeService.
- setFileUploadService(FileUploadService) - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileController
-
Setter for the field fileUploadService.
- setFileURL(String) - Method in class net.sourceforge.seqware.common.business.UploadFile
-
Setter for the field fileURL.
- setFileURL(String) - Method in class net.sourceforge.seqware.common.model.UploadSequence
-
Setter for the field fileURL.
- setFinalized(Boolean) - Method in class io.seqware.webservice.generated.model.Invoice
-
- setFinalized(boolean) - Method in class net.sourceforge.seqware.common.model.Invoice
-
Setter for the field finalized.
- setFinishedTimestamp(Date) - Method in class net.sourceforge.seqware.common.model.Expense
-
Setter for the field
finishedTimestamp.
- setFirstName(String) - Method in class io.seqware.webservice.generated.model.Registration
-
- setFirstName(String) - Method in class net.sourceforge.seqware.common.model.Registration
-
Setter for the field firstName.
- setFirstName(String) - Method in class net.sourceforge.seqware.webservice.dto.OwnerDto
-
Setter for the field firstName.
- setFlowCount(Integer) - Method in class io.seqware.webservice.generated.model.SequencerRun
-
- setFlowCount(Integer) - Method in class net.sourceforge.seqware.common.model.SequencerRun
-
Setter for the field flowCount.
- setFlowCount(Integer) - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
-
Setter for the field flowCount.
- setFlowSequence(String) - Method in class io.seqware.webservice.generated.model.SequencerRun
-
- setFlowSequence(String) - Method in class net.sourceforge.seqware.common.model.SequencerRun
-
Setter for the field flowSequence.
- setFlowSequence(String) - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
-
Setter for the field flowSequence.
- setFolderStore(String) - Method in class net.sourceforge.seqware.common.business.UploadFile
-
Setter for the field folderStore.
- setFolderStore(String) - Method in class net.sourceforge.seqware.common.model.UploadSequence
-
Setter for the field folderStore.
- setForceCopy(boolean) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.SqwFile
-
when forceCopy is true, it will pass "--forcecopy" argument to provisionFileJob
- setForceRunAll(Boolean) - Method in class net.sourceforge.seqware.pipeline.deciders.BasicDecider
-
- setFs_default_name(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Environment
-
- setFs_defaultFS(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Environment
-
- setFs_hdfs_impl(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Environment
-
- setFullyPaid(Boolean) - Method in class io.seqware.webservice.generated.model.Invoice
-
- setFullyPaid(boolean) - Method in class net.sourceforge.seqware.common.model.Invoice
-
Setter for the field fullyPaid.
- setGcrOutputFile(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Command
-
- setGcrSkipIfMissing(boolean) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Command
-
- setGcrSkipIfOutputExists(boolean) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Command
-
- setGroupingStrategy(FindAllTheFiles.Header) - Method in class net.sourceforge.seqware.pipeline.deciders.BasicDecider
-
- setHasMetadataWriteback(boolean) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.AbstractJob
-
- setHasMetadataWriteback(boolean) - Method in interface net.sourceforge.seqware.pipeline.workflowV2.model.Job
-
job specific metadata is not supported yet
- setHasMetadataWriteback(boolean) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.JobBatch
-
- setHbase_master(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Environment
-
- setHbase_zookeeper_property_clientPort(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Environment
-
- setHbase_zookeeper_quorum(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Environment
-
- setHeader(FindAllTheFiles.Header) - Method in class net.sourceforge.seqware.pipeline.deciders.BasicDecider
-
Deprecated.
- setHost(String) - Method in class io.seqware.webservice.generated.model.Workflow
-
- setHost(String) - Method in class io.seqware.webservice.generated.model.WorkflowRun
-
- setHost(String) - Method in class net.sourceforge.seqware.common.model.Workflow
-
Deprecated.
- setHost(String) - Method in class net.sourceforge.seqware.common.model.WorkflowRun
-
Setter for the field host.
- setHost(String) - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowInfo
-
Setter for the field host.
- setHtml(String) - Method in class net.sourceforge.seqware.common.model.SequencerRun
-
Setter for the field html.
- setHtml(String) - Method in class net.sourceforge.seqware.common.model.Study
-
Setter for the field html.
- setHtml(String) - Method in class net.sourceforge.seqware.common.model.WorkflowRun
-
Setter for the field html.
- setId(int) - Method in class io.seqware.webservice.controller.ModelAccessionIDTuple
-
- setId(int) - Method in class io.seqware.webservice.generated.controller.ModelAccessionIDTuple
-
- setId(String) - Method in class io.seqware.webservice.generated.model.ExperimentLink
-
- setId(String) - Method in class io.seqware.webservice.generated.model.IusLink
-
- setId(String) - Method in class io.seqware.webservice.generated.model.LaneLink
-
- setId(String) - Method in class io.seqware.webservice.generated.model.SampleLink
-
- setId(String) - Method in class io.seqware.webservice.generated.model.StudyLink
-
- setId(Integer) - Method in class net.sourceforge.seqware.common.business.UploadFile
-
Setter for the field id.
- setId(String) - Method in class net.sourceforge.seqware.common.model.ExperimentLink
-
Setter for the field id.
- setId(String) - Method in class net.sourceforge.seqware.common.model.IUSLink
-
Setter for the field id.
- setId(String) - Method in class net.sourceforge.seqware.common.model.LaneLink
-
Setter for the field id.
- setId(String) - Method in class net.sourceforge.seqware.common.model.SampleLink
-
Setter for the field id.
- setId(String) - Method in class net.sourceforge.seqware.common.model.StudyLink
-
Setter for the field id.
- setId(int) - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object.PegasusJob
-
set the job id
- setIdentitySamples(Collection<Sample>) - Method in class net.sourceforge.seqware.common.hibernate.reports.WorkflowRunReportRow
-
Setter for the field identitySamples.
- setImmediateInputFiles(Collection<File>) - Method in class net.sourceforge.seqware.common.hibernate.reports.WorkflowRunReportRow
-
Setter for the field immediateInputFiles.
- setIndividualName(String) - Method in class io.seqware.webservice.generated.model.Sample
-
- setIndividualName(String) - Method in class net.sourceforge.seqware.common.model.Sample
-
Setter for the field
individualName.
- setIndividualNumber(String) - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.SampleInfo
-
- setInfo(String) - Method in class net.sourceforge.solexatools.util.PageInfo
-
Setter for the field info.
- setIniFile(String) - Method in class io.seqware.webservice.generated.model.WorkflowRun
-
- setIniFile(String) - Method in class net.sourceforge.seqware.common.model.WorkflowRun
-
Setter for the field iniFile.
- setInputAlgorithm(String) - Method in class io.seqware.webservice.generated.model.Workflow
-
- setInputAlgorithm(String) - Method in class net.sourceforge.seqware.common.model.Workflow
-
Setter for the field inputAlgorithm.
- setInputFileAccessions(Set<Integer>) - Method in class net.sourceforge.seqware.common.model.WorkflowRun
-
- setInstalled(boolean) - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object.WorkflowExecutable
-
- setInstitution(String) - Method in class io.seqware.webservice.generated.model.Registration
-
- setInstitution(String) - Method in class net.sourceforge.seqware.common.model.Registration
-
Setter for the field institution.
- setInstitution(String) - Method in class net.sourceforge.seqware.webservice.dto.OwnerDto
-
Setter for the field institution.
- setInstrumentModel(String) - Method in class io.seqware.webservice.generated.model.Platform
-
- setInstrumentModel(String) - Method in class net.sourceforge.seqware.common.model.Platform
-
Setter for the field instrumentModel.
- setInstrumentName(String) - Method in class io.seqware.webservice.generated.model.SequencerRun
-
- setInstrumentName(String) - Method in class net.sourceforge.seqware.common.model.SequencerRun
-
Setter for the field instrumentName.
- setInstrumentName(String) - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
-
Setter for the field instrumentName.
- setInvitationCode(String) - Method in class io.seqware.webservice.generated.model.Registration
-
- setInvitationCode(String) - Method in class net.sourceforge.seqware.common.model.Registration
-
Setter for the field invitationCode.
- setInvoice(Invoice) - Method in class net.sourceforge.seqware.common.model.Expense
-
Setter for the field
invoice.
- setInvoiceAttributeCollection(Collection<InvoiceAttribute>) - Method in class io.seqware.webservice.generated.model.Invoice
-
- setInvoiceAttributeId(Integer) - Method in class io.seqware.webservice.generated.model.InvoiceAttribute
-
- setInvoiceCollection(Collection<Invoice>) - Method in class io.seqware.webservice.generated.model.Registration
-
- setInvoiceDAO(InvoiceDAO) - Method in class net.sourceforge.seqware.common.business.impl.InvoiceServiceImpl
-
setInvoiceDAO.
- setInvoiceDAO(InvoiceDAO) - Method in interface net.sourceforge.seqware.common.business.InvoiceService
-
setInvoiceDAO.
- setInvoiceId(Invoice) - Method in class io.seqware.webservice.generated.model.Expense
-
- setInvoiceId(Integer) - Method in class io.seqware.webservice.generated.model.Invoice
-
- setInvoiceId(Invoice) - Method in class io.seqware.webservice.generated.model.InvoiceAttribute
-
- setInvoiceId(Integer) - Method in class net.sourceforge.seqware.common.model.Invoice
-
Setter for the field invoiceId.
- setInvoiceService(InvoiceService) - Method in class net.sourceforge.solexatools.webapp.controller.InvoiceDetailsController
-
Setter for the field invoiceService.
- setInvoiceService(InvoiceService) - Method in class net.sourceforge.solexatools.webapp.controller.OpenInvoiceController
-
Setter for the field invoiceService.
- setIsEnd(boolean) - Method in class net.sourceforge.solexatools.util.PageInfo
-
Setter for the field isEnd.
- setIsHasFile(Boolean) - Method in class net.sourceforge.seqware.common.model.Experiment
-
Setter for the field isHasFile.
- setIsHasFile(Boolean) - Method in class net.sourceforge.seqware.common.model.IUS
-
Setter for the field isHasFile.
- setIsHasFile(Boolean) - Method in class net.sourceforge.seqware.common.model.Lane
-
Setter for the field isHasFile.
- setIsHasFile(Boolean) - Method in class net.sourceforge.seqware.common.model.Processing
-
Setter for the field isHasFile.
- setIsHasFile(Boolean) - Method in class net.sourceforge.seqware.common.model.Sample
-
Setter for the field
isHasFile.
- setIsHasFile(Boolean) - Method in class net.sourceforge.seqware.common.model.Study
-
Setter for the field isHasFile.
- setIsHasFile(Boolean) - Method in class net.sourceforge.seqware.common.model.WorkflowRun
-
Setter for the field isHasFile.
- setIsInput(boolean) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.SqwFile
-
isInput = @param isInput
isOutput = !@param isInput
- setIsOutput(boolean) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.SqwFile
-
isInput = !@param isOutput
isOutput = @param isOutput
- setIsPublic(Boolean) - Method in class io.seqware.webservice.generated.model.Sample
-
- setIsSelected(Boolean) - Method in class net.sourceforge.seqware.common.model.Experiment
-
Setter for the field isSelected.
- setIsSelected(Boolean) - Method in class net.sourceforge.seqware.common.model.File
-
Setter for the field isSelected.
- setIsSelected(Boolean) - Method in class net.sourceforge.seqware.common.model.IUS
-
Setter for the field isSelected.
- setIsSelected(Boolean) - Method in class net.sourceforge.seqware.common.model.Lane
-
Setter for the field isSelected.
- setIsSelected(Boolean) - Method in class net.sourceforge.seqware.common.model.Processing
-
Setter for the field isSelected.
- setIsSelected(Boolean) - Method in class net.sourceforge.seqware.common.model.Sample
-
Setter for the field
isSelected.
- setIsSelected(Boolean) - Method in class net.sourceforge.seqware.common.model.Study
-
Setter for the field isSelected.
- setIsSelected(Boolean) - Method in class net.sourceforge.seqware.common.model.WorkflowRun
-
Setter for the field isSelected.
- setIsStart(boolean) - Method in class net.sourceforge.solexatools.util.PageInfo
-
Setter for the field isStart.
- setIus(IUS) - Method in class net.sourceforge.seqware.common.model.FileReportRow
-
Setter for the field ius.
- setIus(IUS) - Method in class net.sourceforge.seqware.common.model.IUSAttribute
-
Setter for the field ius.
- setIus(IUS) - Method in class net.sourceforge.seqware.common.model.IUSLink
-
Setter for the field ius.
- setIUS(SortedSet<IUS>) - Method in class net.sourceforge.seqware.common.model.Lane
-
setIUS.
- setIUS(Set<IUS>) - Method in class net.sourceforge.seqware.common.model.Processing
-
setIUS.
- setIus(IUS) - Method in class net.sourceforge.seqware.common.model.ProcessingIus
-
Setter for the field ius.
- setIUS(SortedSet<IUS>) - Method in class net.sourceforge.seqware.common.model.Sample
-
setIUS.
- setIus(IUS) - Method in class net.sourceforge.seqware.common.model.SampleReportRow
-
Setter for the field ius.
- setIus(IUS) - Method in class net.sourceforge.seqware.common.model.SequencerRunReportId
-
Setter for the field ius.
- setIus(SortedSet<IUS>) - Method in class net.sourceforge.seqware.common.model.WorkflowRun
-
Setter for the field ius.
- setIus(IUS) - Method in class net.sourceforge.solexatools.webapp.metamodel.StudySampleReportFileLineItem
-
Setter for the field ius.
- setIusAttribute(String, String) - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.SampleInfo
-
Adds a new ius attribute if the tag does not exist for this ius, or
changes the value of an existing ius attribute.
- setIusAttributeCollection(Collection<IusAttribute>) - Method in class io.seqware.webservice.generated.model.Ius
-
- setIusAttributeId(Integer) - Method in class io.seqware.webservice.generated.model.IusAttribute
-
- setIusAttributeId(Integer) - Method in class net.sourceforge.seqware.common.model.IUSAttribute
-
Setter for the field iusAttributeId.
- setIusAttributes(Set<IUSAttribute>) - Method in class net.sourceforge.seqware.common.model.IUS
-
Setter for the field iusAttributes.
- setIusAttributes(Set<TagValueUnit>) - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.SampleInfo
-
Set the value of iusAttributes
- setIusCollection(Collection<Ius>) - Method in class io.seqware.webservice.generated.model.Lane
-
- setIusCollection(Collection<Ius>) - Method in class io.seqware.webservice.generated.model.Registration
-
- setIusCollection(Collection<Ius>) - Method in class io.seqware.webservice.generated.model.Sample
-
- setIUSDAO(IUSDAO) - Method in class net.sourceforge.seqware.common.business.impl.FileUploadServiceImpl
-
setIUSDAO.
- setIUSDAO(IUSDAO) - Method in class net.sourceforge.seqware.common.business.impl.IUSServiceImpl
-
setIUSDAO.
- setIUSDAO(IUSDAO) - Method in class net.sourceforge.seqware.common.business.impl.LaneServiceImpl
-
Sets a private member variable with an instance of an implementation of
IUSDAO.
- setIUSDAO(IUSDAO) - Method in interface net.sourceforge.seqware.common.business.IUSService
-
setIUSDAO.
- setIusDescription(String) - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.SampleInfo
-
Set the value of iusDescription
- setIusId(Integer) - Method in class io.seqware.webservice.generated.model.FileReport
-
- setIusId(Integer) - Method in class io.seqware.webservice.generated.model.Ius
-
- setIusId(Ius) - Method in class io.seqware.webservice.generated.model.IusAttribute
-
- setIusId(Ius) - Method in class io.seqware.webservice.generated.model.IusLink
-
- setIusId(Ius) - Method in class io.seqware.webservice.generated.model.IusWorkflowRuns
-
- setIusId(Ius) - Method in class io.seqware.webservice.generated.model.ProcessingIus
-
- setIusId(Integer) - Method in class io.seqware.webservice.generated.model.SampleReport
-
- setIusId(Integer) - Method in class net.sourceforge.seqware.common.model.IUS
-
Setter for the field iusId.
- setIusLinkCollection(Collection<IusLink>) - Method in class io.seqware.webservice.generated.model.Ius
-
- setIusLinkId(Integer) - Method in class io.seqware.webservice.generated.model.IusLink
-
- setIusLinkId(int) - Method in class net.sourceforge.seqware.common.model.IUSLink
-
Setter for the field iusLinkId.
- setIusLinks(Set<IUSLink>) - Method in class net.sourceforge.seqware.common.model.IUS
-
Setter for the field iusLinks.
- setIusName(String) - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.SampleInfo
-
Set the value of iusName
- setIusService(IUSService) - Method in class net.sourceforge.seqware.common.ContextImpl
-
Setter for the field iusService.
- setIusService(IUSService) - Method in class net.sourceforge.solexatools.webapp.controller.BulkDownloadListDetailsController
-
Setter for the field iusService.
- setIUSService(IUSService) - Method in class net.sourceforge.solexatools.webapp.controller.BulkDownloadListDetailsController
-
setIUSService.
- setIUSService(IUSService) - Method in class net.sourceforge.solexatools.webapp.controller.EntityController
-
setIUSService.
- setIusService(IUSService) - Method in class net.sourceforge.solexatools.webapp.controller.IUSController
-
Setter for the field iusService.
- setIUSService(IUSService) - Method in class net.sourceforge.solexatools.webapp.controller.IUSController
-
setIUSService.
- setIusService(IUSService) - Method in class net.sourceforge.solexatools.webapp.controller.IUSSetupController
-
Setter for the field iusService.
- setIusService(IUSService) - Method in class net.sourceforge.solexatools.webapp.controller.LaneSampleAssociateController
-
Setter for the field iusService.
- setIUSService(IUSService) - Method in class net.sourceforge.solexatools.webapp.controller.LaneSampleAssociateController
-
setIUSService.
- setIusService(IUSService) - Method in class net.sourceforge.solexatools.webapp.controller.LaunchWorkflowListDetailsController
-
Setter for the field iusService.
- setIUSService(IUSService) - Method in class net.sourceforge.solexatools.webapp.controller.LaunchWorkflowListDetailsController
-
setIUSService.
- setIUSService(IUSService) - Method in class net.sourceforge.solexatools.webapp.controller.SearchResultsListController
-
setIUSService.
- setIusService(IUSService) - Method in class net.sourceforge.solexatools.webapp.controller.SelectInputListController
-
Setter for the field iusService.
- setIUSService(IUSService) - Method in class net.sourceforge.solexatools.webapp.controller.SelectInputListController
-
setIUSService.
- setIusService(IUSService) - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunListDetailsController
-
Setter for the field iusService.
- setIUSService(IUSService) - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunListDetailsController
-
setIUSService.
- setIusService(IUSService) - Method in class net.sourceforge.solexatools.webapp.controller.StudyListDetailsController
-
Setter for the field iusService.
- setIUSService(IUSService) - Method in class net.sourceforge.solexatools.webapp.controller.StudyListDetailsController
-
setIUSService.
- setIUSService(IUSService) - Method in class net.sourceforge.solexatools.webapp.controller.StudyListDetailsFlatController
-
setIUSService.
- setIusService(IUSService) - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileController
-
Setter for the field iusService.
- setIUSService(IUSService) - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileController
-
setIUSService.
- setIusService(IUSService) - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileSetupController
-
Setter for the field iusService.
- setIUSService(IUSService) - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileSetupController
-
setIUSService.
- setIusSkip(boolean) - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.SampleInfo
-
Set the value of iusSkip
- setIusSwas(Set<String>) - Method in class net.sourceforge.seqware.common.business.impl.ValidationReportServiceImpl.ReportEntry
-
- setIusWorkflowRunsCollection(Collection<IusWorkflowRuns>) - Method in class io.seqware.webservice.generated.model.Ius
-
- setIusWorkflowRunsCollection(Collection<IusWorkflowRuns>) - Method in class io.seqware.webservice.generated.model.WorkflowRun
-
- setIusWorkflowRunsId(Integer) - Method in class io.seqware.webservice.generated.model.IusWorkflowRuns
-
- setJoinDevelopersMailingList(boolean) - Method in class net.sourceforge.seqware.common.model.Registration
-
Setter for the field joinDevelopersMailingList.
- setJoinUsersMailingList(boolean) - Method in class net.sourceforge.seqware.common.model.Registration
-
Setter for the field joinUsersMailingList.
- setKey(String) - Method in class io.seqware.webservice.generated.model.WorkflowParam
-
- setKey(String) - Method in class io.seqware.webservice.generated.model.WorkflowRunParam
-
- setKey(String) - Method in class net.sourceforge.seqware.common.model.WorkflowParam
-
Setter for the field key.
- setKey(String) - Method in class net.sourceforge.seqware.common.model.WorkflowRunParam
-
Setter for the field key.
- setKey(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Argument
-
Setter for the field key.
- setKey(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.JobProfile
-
Setter for the field key.
- setLabel(String) - Method in class io.seqware.webservice.generated.model.ExperimentLink
-
- setLabel(String) - Method in class io.seqware.webservice.generated.model.IusLink
-
- setLabel(String) - Method in class io.seqware.webservice.generated.model.LaneLink
-
- setLabel(String) - Method in class io.seqware.webservice.generated.model.ProcessingExperiments
-
- setLabel(String) - Method in class io.seqware.webservice.generated.model.ProcessingIus
-
- setLabel(String) - Method in class io.seqware.webservice.generated.model.ProcessingLanes
-
- setLabel(String) - Method in class io.seqware.webservice.generated.model.ProcessingSamples
-
- setLabel(String) - Method in class io.seqware.webservice.generated.model.ProcessingSequencerRuns
-
- setLabel(String) - Method in class io.seqware.webservice.generated.model.ProcessingStudies
-
- setLabel(String) - Method in class io.seqware.webservice.generated.model.SampleLink
-
- setLabel(String) - Method in class io.seqware.webservice.generated.model.StudyLink
-
- setLabel(String) - Method in class net.sourceforge.seqware.common.model.ExperimentLink
-
Setter for the field label.
- setLabel(String) - Method in class net.sourceforge.seqware.common.model.IUSLink
-
Setter for the field label.
- setLabel(String) - Method in class net.sourceforge.seqware.common.model.LaneLink
-
Setter for the field label.
- setLabel(String) - Method in class net.sourceforge.seqware.common.model.ProcessingExperiments
-
Setter for the field label.
- setLabel(String) - Method in class net.sourceforge.seqware.common.model.ProcessingIus
-
Setter for the field label.
- setLabel(String) - Method in class net.sourceforge.seqware.common.model.ProcessingLanes
-
Setter for the field label.
- setLabel(String) - Method in class net.sourceforge.seqware.common.model.ProcessingSamples
-
Setter for the field label.
- setLabel(String) - Method in class net.sourceforge.seqware.common.model.ProcessingSequencerRuns
-
Setter for the field label.
- setLabel(String) - Method in class net.sourceforge.seqware.common.model.ProcessingStudies
-
Setter for the field label.
- setLabel(String) - Method in class net.sourceforge.seqware.common.model.SampleLink
-
Setter for the field label.
- setLabel(String) - Method in class net.sourceforge.seqware.common.model.StudyLink
-
Setter for the field label.
- setLane(Lane) - Method in class net.sourceforge.seqware.common.model.FileReportRow
-
Setter for the field lane.
- setLane(Lane) - Method in class net.sourceforge.seqware.common.model.IUS
-
Setter for the field lane.
- setLane(Lane) - Method in class net.sourceforge.seqware.common.model.LaneAttribute
-
Setter for the field lane.
- setLane(Lane) - Method in class net.sourceforge.seqware.common.model.LaneLink
-
Setter for the field lane.
- setLane(Lane) - Method in class net.sourceforge.seqware.common.model.ProcessingLanes
-
Setter for the field lane.
- setLane(Lane) - Method in class net.sourceforge.seqware.common.model.SampleReportRow
-
Setter for the field lane.
- setLane(Lane) - Method in class net.sourceforge.seqware.common.model.SequencerRunReportId
-
Setter for the field lane.
- setLane(Lane) - Method in class net.sourceforge.seqware.common.model.ShareLane
-
Setter for the field lane.
- setLane(Integer) - Method in class net.sourceforge.seqware.pipeline.plugins.filelinker.FileLinkerLine
-
- setLane1(Lane) - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
-
Setter for the field lane1.
- setLane2(Lane) - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
-
Setter for the field lane2.
- setLane3(Lane) - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
-
Setter for the field lane3.
- setLane4(Lane) - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
-
Setter for the field lane4.
- setLane5(Lane) - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
-
Setter for the field lane5.
- setLane6(Lane) - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
-
Setter for the field lane6.
- setLane7(Lane) - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
-
Setter for the field lane7.
- setLane8(Lane) - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
-
Setter for the field lane8.
- setLane_url(String) - Method in class net.sourceforge.seqware.webservice.dto.IusDto
-
Setter for the field lane_url.
- setLaneAttribute(String, String) - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.LaneInfo
-
Adds a new lane attribute if the tag does not exist for this lane, or
changes the value of an existing lane attribute.
- setLaneAttributeCollection(Collection<LaneAttribute>) - Method in class io.seqware.webservice.generated.model.Lane
-
- setLaneAttributeId(Integer) - Method in class io.seqware.webservice.generated.model.LaneAttribute
-
- setLaneAttributeId(Integer) - Method in class net.sourceforge.seqware.common.model.LaneAttribute
-
Setter for the field laneAttributeId.
- setLaneAttributes(Set<LaneAttribute>) - Method in class net.sourceforge.seqware.common.model.Lane
-
Setter for the field laneAttributes.
- setLaneAttributes(Set<TagValueUnit>) - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.LaneInfo
-
- setLaneCollection(Collection<Lane>) - Method in class io.seqware.webservice.generated.model.LaneType
-
- setLaneCollection(Collection<Lane>) - Method in class io.seqware.webservice.generated.model.LibrarySelection
-
- setLaneCollection(Collection<Lane>) - Method in class io.seqware.webservice.generated.model.LibrarySource
-
- setLaneCollection(Collection<Lane>) - Method in class io.seqware.webservice.generated.model.LibraryStrategy
-
- setLaneCollection(Collection<Lane>) - Method in class io.seqware.webservice.generated.model.Organism
-
- setLaneCollection(Collection<Lane>) - Method in class io.seqware.webservice.generated.model.Registration
-
- setLaneCollection(Collection<Lane>) - Method in class io.seqware.webservice.generated.model.Sample
-
- setLaneCollection(Collection<Lane>) - Method in class io.seqware.webservice.generated.model.SequencerRun
-
- setLaneCollection(Collection<Lane>) - Method in class io.seqware.webservice.generated.model.StudyType
-
- setLaneCount(int) - Method in class net.sourceforge.seqware.common.model.SequencerRunWizardDTO
-
Setter for the field laneCount.
- setLaneCycleDescriptor(String) - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.LaneInfo
-
Set the value of laneCycleDescriptor
- setLaneDAO(LaneDAO) - Method in class net.sourceforge.seqware.common.business.impl.FileUploadServiceImpl
-
Setter for the field laneDAO.
- setLaneDAO(LaneDAO) - Method in class net.sourceforge.seqware.common.business.impl.LaneServiceImpl
-
setLaneDAO.
- setLaneDAO(LaneDAO) - Method in class net.sourceforge.seqware.common.business.impl.SequencerRunServiceImpl
-
Sets a private member variable with an instance of an implementation of
LaneDAO.
- setLaneDAO(LaneDAO) - Method in interface net.sourceforge.seqware.common.business.LaneService
-
setLaneDAO.
- setLaneDescription(String) - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.LaneInfo
-
Set the value of laneDescription
- setLaneForSequrncerRun(Lane, HttpServletRequest) - Static method in class net.sourceforge.solexatools.util.SetNodeIdInSession
-
setLaneForSequrncerRun.
- setLaneForStudy(Lane, HttpServletRequest) - Static method in class net.sourceforge.solexatools.util.SetNodeIdInSession
-
setLaneForStudy.
- setLaneId(Integer) - Method in class io.seqware.webservice.generated.model.FileReport
-
- setLaneId(Lane) - Method in class io.seqware.webservice.generated.model.Ius
-
- setLaneId(Integer) - Method in class io.seqware.webservice.generated.model.Lane
-
- setLaneId(Lane) - Method in class io.seqware.webservice.generated.model.LaneAttribute
-
- setLaneId(Lane) - Method in class io.seqware.webservice.generated.model.LaneLink
-
- setLaneId(Lane) - Method in class io.seqware.webservice.generated.model.LaneWorkflowRuns
-
- setLaneId(Lane) - Method in class io.seqware.webservice.generated.model.ProcessingLanes
-
- setLaneId(Integer) - Method in class io.seqware.webservice.generated.model.SampleReport
-
- setLaneId(Lane) - Method in class io.seqware.webservice.generated.model.ShareLane
-
- setLaneId(Integer) - Method in class net.sourceforge.seqware.common.model.Lane
-
Setter for the field laneId.
- setLaneIndex(Integer) - Method in class io.seqware.webservice.generated.model.Lane
-
- setLaneIndex(Integer) - Method in class net.sourceforge.seqware.common.model.Lane
-
Setter for the field laneIndex.
- setLaneLinkCollection(Collection<LaneLink>) - Method in class io.seqware.webservice.generated.model.Lane
-
- setLaneLinkId(Integer) - Method in class io.seqware.webservice.generated.model.LaneLink
-
- setLaneLinkId(int) - Method in class net.sourceforge.seqware.common.model.LaneLink
-
Setter for the field laneLinkId.
- setLaneLinks(Set<LaneLink>) - Method in class net.sourceforge.seqware.common.model.Lane
-
Setter for the field laneLinks.
- setLaneName(String) - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.LaneInfo
-
Set the value of laneName
- setLaneNumber(String) - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.LaneInfo
-
Set the value of laneNumber, and sets the 'geo_lane' attribute.
- setLanes(Set<Lane>) - Method in class net.sourceforge.seqware.common.model.Processing
-
Setter for the field lanes.
- setLanes(SortedSet<Lane>) - Method in class net.sourceforge.seqware.common.model.Sample
-
Setter for the field
lanes.
- setLanes(SortedSet<Lane>) - Method in class net.sourceforge.seqware.common.model.SequencerRun
-
Setter for the field lanes.
- setLanes(SortedSet<Lane>) - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
-
Setter for the field lanes.
- setLanes(SortedSet<Lane>) - Method in class net.sourceforge.seqware.common.model.WorkflowRun
-
Setter for the field lanes.
- setLanes(Set<LaneInfo>) - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.RunInfo
-
Set the value of lanes
- setLaneService(LaneService) - Method in class net.sourceforge.seqware.common.ContextImpl
-
Setter for the field laneService.
- setLaneService(LaneService) - Method in class net.sourceforge.solexatools.validation.LaneValidator
-
Setter for the field laneService.
- setLaneService(LaneService) - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysBulkDownloadListDetailsController
-
Setter for the field laneService.
- setLaneService(LaneService) - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysListDetailsController
-
Setter for the field laneService.
- setLaneService(LaneService) - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysRunningListDetailsController
-
Setter for the field laneService.
- setLaneService(LaneService) - Method in class net.sourceforge.solexatools.webapp.controller.BulkDownloadListDetailsController
-
Setter for the field laneService.
- setLaneService(LaneService) - Method in class net.sourceforge.solexatools.webapp.controller.DownloadFileListController
-
Setter for the field laneService.
- setLaneService(LaneService) - Method in class net.sourceforge.solexatools.webapp.controller.EntityController
-
Setter for the field laneService.
- setLaneService(LaneService) - Method in class net.sourceforge.solexatools.webapp.controller.LaneController
-
Setter for the field laneService.
- setLaneService(LaneService) - Method in class net.sourceforge.solexatools.webapp.controller.LaneSampleAssociateController
-
Setter for the field laneService.
- setLaneService(LaneService) - Method in class net.sourceforge.solexatools.webapp.controller.LaneSampleAssociateSetupController
-
Setter for the field laneService.
- setLaneService(LaneService) - Method in class net.sourceforge.solexatools.webapp.controller.LaneSetupController
-
Setter for the field laneService.
- setLaneService(LaneService) - Method in class net.sourceforge.solexatools.webapp.controller.LaunchWorkflowListDetailsController
-
Setter for the field laneService.
- setLaneService(LaneService) - Method in class net.sourceforge.solexatools.webapp.controller.SampleSetupController
-
Setter for the field laneService.
- setLaneService(LaneService) - Method in class net.sourceforge.solexatools.webapp.controller.SaveOpenNodeController
-
Setter for the field laneService.
- setLaneService(LaneService) - Method in class net.sourceforge.solexatools.webapp.controller.SearchResultsListController
-
Setter for the field laneService.
- setLaneService(LaneService) - Method in class net.sourceforge.solexatools.webapp.controller.SelectInputListController
-
Setter for the field laneService.
- setLaneService(LaneService) - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunController
-
Setter for the field laneService.
- setLaneService(LaneService) - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunControllerDTO
-
Setter for the field laneService.
- setLaneService(LaneService) - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunListDetailsController
-
Setter for the field laneService.
- setLaneService(LaneService) - Method in class net.sourceforge.solexatools.webapp.controller.StudyListDetailsController
-
Setter for the field laneService.
- setLaneService(LaneService) - Method in class net.sourceforge.solexatools.webapp.controller.StudyListDetailsFlatController
-
Setter for the field laneService.
- setLaneService(LaneService) - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileController
-
Setter for the field laneService.
- setLaneService(LaneService) - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileSetupController
-
Setter for the field laneService.
- setLaneService(LaneService) - Method in class net.sourceforge.solexatools.webapp.controller.UploadSequenceController
-
Setter for the field laneService.
- setLanesForView(SortedSet<Lane>) - Method in class net.sourceforge.seqware.common.model.Sample
-
setLanesForView.
- setLaneSkip(Boolean) - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.LaneInfo
-
Set the value of laneSkip
- setLaneString(String) - Method in class net.sourceforge.seqware.pipeline.plugins.filelinker.FileLinkerLine
-
- setLaneSwas(Set<String>) - Method in class net.sourceforge.seqware.common.business.impl.ValidationReportServiceImpl.ReportEntry
-
- setLaneTypeId(Integer) - Method in class io.seqware.webservice.generated.model.LaneType
-
- setLaneWorkflowRunsCollection(Collection<LaneWorkflowRuns>) - Method in class io.seqware.webservice.generated.model.Lane
-
- setLaneWorkflowRunsCollection(Collection<LaneWorkflowRuns>) - Method in class io.seqware.webservice.generated.model.WorkflowRun
-
- setLaneWorkflowRunsId(Integer) - Method in class io.seqware.webservice.generated.model.LaneWorkflowRuns
-
- setLastName(String) - Method in class io.seqware.webservice.generated.model.Registration
-
- setLastName(String) - Method in class net.sourceforge.seqware.common.model.Registration
-
Setter for the field lastName.
- setLastName(String) - Method in class net.sourceforge.seqware.webservice.dto.OwnerDto
-
Setter for the field lastName.
- setLastUpdateTstmp(Date) - Method in class io.seqware.webservice.generated.model.Registration
-
- setLatestDate(Date) - Method in class net.sourceforge.seqware.common.hibernate.WorkflowRunReport
-
Set the value of latestDate.
- setLayout(String) - Method in class io.seqware.webservice.generated.model.ExperimentLibraryDesign
-
- setLayout(String) - Method in class net.sourceforge.seqware.common.model.ExperimentLibraryDesign
-
Setter for the field layout.
- setLength(Integer) - Method in class io.seqware.webservice.generated.model.ExperimentSpotDesignReadSpec
-
- setLength(Integer) - Method in class net.sourceforge.seqware.common.model.ExperimentSpotDesignReadSpec
-
Setter for the field length.
- setLibraryId(String) - Method in class net.sourceforge.seqware.webservice.dto.LibraryIdentityDto
-
Setter for the field libraryId.
- setLibrarySamples(Collection<Sample>) - Method in class net.sourceforge.seqware.common.hibernate.reports.WorkflowRunReportRow
-
Setter for the field librarySamples.
- setLibrarySelection(LibrarySelection) - Method in class io.seqware.webservice.generated.model.Lane
-
- setLibrarySelection(LibrarySelection) - Method in class net.sourceforge.seqware.common.model.Lane
-
- setLibrarySelectionAcc(int) - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.LaneInfo
-
Set the value of librarySelectionAcc
- setLibrarySelectionDAO(LibrarySelectionDAO) - Method in class net.sourceforge.seqware.common.business.impl.LibrarySelectionServiceImpl
-
setLibrarySelectionDAO.
- setLibrarySelectionDAO(LibrarySelectionDAO) - Method in interface net.sourceforge.seqware.common.business.LibrarySelectionService
-
setLibrarySelectionDAO.
- setLibrarySelectionId(Integer) - Method in class io.seqware.webservice.generated.model.LibrarySelection
-
- setLibrarySelectionId(Integer) - Method in class net.sourceforge.seqware.common.model.LibrarySelection
-
Setter for the field librarySelectionId.
- setLibrarySelectionService(LibrarySelectionService) - Method in class net.sourceforge.seqware.common.ContextImpl
-
- setLibrarySelectionService(LibrarySelectionService) - Method in class net.sourceforge.solexatools.webapp.controller.ExperimentController
-
Setter for the field librarySelectionService.
- setLibrarySelectionService(LibrarySelectionService) - Method in class net.sourceforge.solexatools.webapp.controller.ExperimentSetupController
-
Setter for the field librarySelectionService.
- setLibraryService(LibraryService) - Method in class net.sourceforge.seqware.common.ContextImpl
-
Setter for the field libraryService.
- setLibrarySizeCode(String) - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.SampleInfo
-
Sets the library size code and sets the 'geo_library_size_code'
attribute.
- setLibrarySource(LibrarySource) - Method in class io.seqware.webservice.generated.model.Lane
-
- setLibrarySource(LibrarySource) - Method in class net.sourceforge.seqware.common.model.Lane
-
- setLibrarySourceAcc(int) - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.LaneInfo
-
Set the value of librarySourceAcc
- setLibrarySourceDAO(LibrarySourceDAO) - Method in class net.sourceforge.seqware.common.business.impl.LibrarySourceServiceImpl
-
setLibrarySourceDAO.
- setLibrarySourceDAO(LibrarySourceDAO) - Method in interface net.sourceforge.seqware.common.business.LibrarySourceService
-
setLibrarySourceDAO.
- setLibrarySourceId(Integer) - Method in class io.seqware.webservice.generated.model.LibrarySource
-
- setLibrarySourceId(Integer) - Method in class net.sourceforge.seqware.common.model.LibrarySource
-
Setter for the field librarySourceId.
- setLibrarySourceService(LibrarySourceService) - Method in class net.sourceforge.seqware.common.ContextImpl
-
- setLibrarySourceService(LibrarySourceService) - Method in class net.sourceforge.solexatools.webapp.controller.ExperimentController
-
Setter for the field librarySourceService.
- setLibrarySourceService(LibrarySourceService) - Method in class net.sourceforge.solexatools.webapp.controller.ExperimentSetupController
-
Setter for the field librarySourceService.
- setLibrarySourceTemplateType(String) - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.SampleInfo
-
Set the value of librarySourceTemplateType sets the
'geo_library_source_template_type' attribute.
- setLibraryStrategy(LibraryStrategy) - Method in class io.seqware.webservice.generated.model.Lane
-
- setLibraryStrategy(LibraryStrategy) - Method in class net.sourceforge.seqware.common.model.Lane
-
- setLibraryStrategyAcc(int) - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.LaneInfo
-
Set the value of libraryStrategyAcc
- setLibraryStrategyDAO(LibraryStrategyDAO) - Method in class net.sourceforge.seqware.common.business.impl.LibraryStrategyServiceImpl
-
setLibraryStrategyDAO.
- setLibraryStrategyDAO(LibraryStrategyDAO) - Method in interface net.sourceforge.seqware.common.business.LibraryStrategyService
-
setLibraryStrategyDAO.
- setLibraryStrategyId(Integer) - Method in class io.seqware.webservice.generated.model.LibraryStrategy
-
- setLibraryStrategyId(Integer) - Method in class net.sourceforge.seqware.common.model.LibraryStrategy
-
Setter for the field libraryStrategyId.
- setLibraryStrategyService(LibraryStrategyService) - Method in class net.sourceforge.seqware.common.ContextImpl
-
- setLibraryStrategyService(LibraryStrategyService) - Method in class net.sourceforge.solexatools.webapp.controller.ExperimentController
-
Setter for the field libraryStrategyService.
- setLibraryStrategyService(LibraryStrategyService) - Method in class net.sourceforge.solexatools.webapp.controller.ExperimentSetupController
-
Setter for the field libraryStrategyService.
- setLibraryType(String) - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.SampleInfo
-
Sets the library type and sets the 'geo_library_type' attribute .
- setLibraryType(String) - Method in class net.sourceforge.solexatools.webapp.metamodel.StudySampleReportFileLineItem
-
Setter for the field libraryType.
- setLimsAdmin(boolean) - Method in class io.seqware.webservice.generated.model.Registration
-
- setLIMSAdmin(boolean) - Method in class net.sourceforge.seqware.common.model.Registration
-
setLIMSAdmin.
- setList(List<ExperimentLibraryDesign>) - Method in class net.sourceforge.seqware.common.model.lists.ExperimentLibraryDesignList
-
setList.
- setList(List<Experiment>) - Method in class net.sourceforge.seqware.common.model.lists.ExperimentList
-
setList.
- setList(List<ExperimentSpotDesign>) - Method in class net.sourceforge.seqware.common.model.lists.ExperimentSpotDesignList
-
setList.
- setList(List<ExperimentSpotDesignReadSpec>) - Method in class net.sourceforge.seqware.common.model.lists.ExperimentSpotDesignReadSpecList
-
setList.
- setList(List<File>) - Method in class net.sourceforge.seqware.common.model.lists.FileList
-
setList.
- setList(List<Integer>) - Method in class net.sourceforge.seqware.common.model.lists.IntegerList
-
setList.
- setList(List<IUS>) - Method in class net.sourceforge.seqware.common.model.lists.IUSList
-
setList.
- setList(List<Lane>) - Method in class net.sourceforge.seqware.common.model.lists.LaneList
-
setList.
- setList(List<LibrarySelection>) - Method in class net.sourceforge.seqware.common.model.lists.LibrarySelectionList
-
setList.
- setList(List<LibrarySource>) - Method in class net.sourceforge.seqware.common.model.lists.LibrarySourceList
-
setList.
- setList(List<LibraryStrategy>) - Method in class net.sourceforge.seqware.common.model.lists.LibraryStrategyList
-
setList.
- setList(List<Organism>) - Method in class net.sourceforge.seqware.common.model.lists.OrganismList
-
setList.
- setList(List<Platform>) - Method in class net.sourceforge.seqware.common.model.lists.PlatformList
-
setList.
- setList(List<Processing>) - Method in class net.sourceforge.seqware.common.model.lists.ProcessingList
-
setList.
- setList(List<ReturnValue>) - Method in class net.sourceforge.seqware.common.model.lists.ReturnValueList
-
setList.
- setList(List<Sample>) - Method in class net.sourceforge.seqware.common.model.lists.SampleList
-
setList.
- setList(List<SequencerRun>) - Method in class net.sourceforge.seqware.common.model.lists.SequencerRunList
-
setList.
- setList(List<Study>) - Method in class net.sourceforge.seqware.common.model.lists.StudyList
-
setList.
- setList(List<StudyType>) - Method in class net.sourceforge.seqware.common.model.lists.StudyTypeList
-
setList.
- setList(List<Workflow>) - Method in class net.sourceforge.seqware.common.model.lists.WorkflowList
-
setList.
- setList(List<WorkflowParam>) - Method in class net.sourceforge.seqware.common.model.lists.WorkflowParamList
-
setList.
- setList(List<WorkflowParamValue>) - Method in class net.sourceforge.seqware.common.model.lists.WorkflowParamValueList
-
setList.
- setList(Collection<WorkflowRun>) - Method in class net.sourceforge.seqware.common.model.lists.WorkflowRunList
-
setList.
- setList(List<WorkflowRun>) - Method in class net.sourceforge.seqware.common.model.lists.WorkflowRunList2
-
setList.
- setLocal() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.AbstractJob
-
- setLocal(boolean) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.AbstractJob
-
- setLocal() - Method in interface net.sourceforge.seqware.pipeline.workflowV2.model.Job
-
Sets this job to run locally.
- setLocal(boolean) - Method in interface net.sourceforge.seqware.pipeline.workflowV2.model.Job
-
Sets whether this job should run locally.
- setLocal() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.JobBatch
-
- setLocal(boolean) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.JobBatch
-
- setMapred_job_tracker(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Environment
-
- setMaxMemory(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.AbstractJob
-
- setMaxMemory(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Command
-
- setMaxMemory(String) - Method in interface net.sourceforge.seqware.pipeline.workflowV2.model.Job
-
set max memory
- setMd5sum(String) - Method in class io.seqware.webservice.generated.model.File
-
- setMd5sum(String) - Method in class net.sourceforge.seqware.common.model.File
-
Setter for the field md5sum.
- setMd5sum(String) - Method in class net.sourceforge.seqware.common.module.FileMetadata
-
- setMd5sum(String) - Method in class net.sourceforge.seqware.pipeline.plugins.filelinker.FileLinkerLine
-
- setMd5sum(String) - Method in class net.sourceforge.seqware.webservice.dto.FileDto
-
Setter for the field md5sum.
- setMemory(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Environment
-
- setMemReq(String) - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowInfo
-
Setter for the field memReq.
- setMetadata(Metadata) - Method in class net.sourceforge.seqware.pipeline.bundle.Bundle
-
Setter for the field metadata.
- setMetadata(Metadata) - Method in interface net.sourceforge.seqware.pipeline.decider.DeciderInterface
-
Lets you set the metadata object
- setMetadata(Metadata) - Method in class net.sourceforge.seqware.pipeline.module.Module
-
Setter for the field metadata.
- setMetadata(Metadata) - Method in class net.sourceforge.seqware.pipeline.plugin.Plugin
-
Lets you set the metadata object
- setMetadata(Metadata) - Method in interface net.sourceforge.seqware.pipeline.plugin.PluginInterface
-
Lets you set the metadata object
- setMetadata(Metadata) - Method in class net.sourceforge.seqware.pipeline.plugins.HelloWorld
-
Lets you set the metadata object
- setMetadata(Metadata) - Method in class net.sourceforge.seqware.pipeline.plugins.MarkdownPlugin
-
Lets you set the metadata object
- setMetadata(Metadata) - Method in class net.sourceforge.seqware.pipeline.plugins.WorkflowRunFilesInitialPopulationPlugin
-
Lets you set the metadata object
- setMetadataOutputPrefix(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object.OozieProvisionFileJob
-
- setMetadataOutputPrefix(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object.ProvisionFilesJob
-
- setMetadataWriteback(Boolean) - Method in class net.sourceforge.seqware.pipeline.deciders.BasicDecider
-
- setMetadataWriteBack(boolean) - Method in class net.sourceforge.seqware.pipeline.workflowV2.AbstractWorkflowDataModel
-
need metadata writeback? user can override this setting by using --no-metadata or --metadata from command line
- setMetadataWriteback(boolean) - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object.OozieJob
-
- setMetadataWriteback(boolean) - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object.PegasusJob
-
- setMetaType(String) - Method in class io.seqware.webservice.generated.model.File
-
- setMetaType(String) - Method in class io.seqware.webservice.generated.model.FileType
-
- setMetaType(String) - Method in class net.sourceforge.seqware.common.model.File
-
Setter for the field metaType.
- setMetaType(String) - Method in class net.sourceforge.seqware.common.model.FileType
-
Setter for the field metaType.
- setMetaType(String) - Method in class net.sourceforge.seqware.common.module.FileMetadata
-
- setMetaType(List<String>) - Method in class net.sourceforge.seqware.pipeline.deciders.BasicDecider
-
- setMetaType(String) - Method in class net.sourceforge.seqware.webservice.dto.FileDto
-
Setter for the field metaType.
- setMetaws(Metadata) - Method in class net.sourceforge.seqware.pipeline.deciders.BasicDecider
-
- setMimeType(String) - Method in class net.sourceforge.seqware.pipeline.plugins.filelinker.FileLinkerLine
-
- setName(String) - Method in class io.seqware.webservice.generated.model.Experiment
-
- setName(String) - Method in class io.seqware.webservice.generated.model.ExperimentLibraryDesign
-
- setName(String) - Method in class io.seqware.webservice.generated.model.Ius
-
- setName(String) - Method in class io.seqware.webservice.generated.model.Lane
-
- setName(String) - Method in class io.seqware.webservice.generated.model.LaneType
-
- setName(String) - Method in class io.seqware.webservice.generated.model.LibrarySelection
-
- setName(String) - Method in class io.seqware.webservice.generated.model.LibrarySource
-
- setName(String) - Method in class io.seqware.webservice.generated.model.LibraryStrategy
-
- setName(String) - Method in class io.seqware.webservice.generated.model.Organism
-
- setName(String) - Method in class io.seqware.webservice.generated.model.Platform
-
- setName(String) - Method in class io.seqware.webservice.generated.model.Sample
-
- setName(String) - Method in class io.seqware.webservice.generated.model.SequencerRun
-
- setName(String) - Method in class io.seqware.webservice.generated.model.StudyType
-
- setName(String) - Method in class io.seqware.webservice.generated.model.Workflow
-
- setName(String) - Method in class io.seqware.webservice.generated.model.WorkflowRun
-
- setName(String) - Method in class net.sourceforge.seqware.common.model.Experiment
-
Setter for the field name.
- setName(String) - Method in class net.sourceforge.seqware.common.model.ExperimentLibraryDesign
-
Setter for the field name.
- setName(String) - Method in class net.sourceforge.seqware.common.model.IUS
-
Setter for the field name.
- setName(String) - Method in class net.sourceforge.seqware.common.model.Lane
-
Setter for the field name.
- setName(String) - Method in class net.sourceforge.seqware.common.model.LibrarySelection
-
Setter for the field name.
- setName(String) - Method in class net.sourceforge.seqware.common.model.LibrarySource
-
Setter for the field name.
- setName(String) - Method in class net.sourceforge.seqware.common.model.LibraryStrategy
-
Setter for the field name.
- setName(String) - Method in class net.sourceforge.seqware.common.model.Organism
-
Setter for the field name.
- setName(String) - Method in class net.sourceforge.seqware.common.model.Platform
-
Setter for the field name.
- setName(String) - Method in class net.sourceforge.seqware.common.model.Sample
-
Setter for the field
name.
- setName(String) - Method in class net.sourceforge.seqware.common.model.SequencerRun
-
Setter for the field name.
- setName(String) - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
-
Setter for the field name.
- setName(String) - Method in class net.sourceforge.seqware.common.model.StudyType
-
Setter for the field name.
- setName(String) - Method in class net.sourceforge.seqware.common.model.Workflow
-
Setter for the field name.
- setName(String) - Method in class net.sourceforge.seqware.common.model.WorkflowRun
-
Setter for the field name.
- setName(String) - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowInfo
-
Setter for the field name.
- setName(String) - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.SampleInfo
-
Set the value of name
- setName(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.AbstractWorkflowDataModel
-
set the workflow name
- setName(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object.WorkflowExecutable
-
- setName(String) - Method in class net.sourceforge.seqware.webservice.dto.AttributeDto
-
Setter for the field name.
- setName(String) - Method in class net.sourceforge.seqware.webservice.dto.LibraryDto
-
Setter for the field name.
- setName(String) - Method in class net.sourceforge.seqware.webservice.dto.OrganismDto
-
Setter for the field name.
- setName(String) - Method in class net.sourceforge.solexatools.webapp.metamodel.Flexigrid.ColumnModel
-
- setNameNode(String) - Method in class net.sourceforge.seqware.common.business.UploadFile
-
Setter for the field nameNode.
- setNamespace(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object.WorkflowExecutable
-
- setNamespace(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.JobProfile
-
setNamespace.
- setNamespace(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Requirement
-
- setNcbiTaxid(Integer) - Method in class io.seqware.webservice.generated.model.Organism
-
- setNcbiTaxId(Integer) - Method in class net.sourceforge.seqware.common.model.Organism
-
Setter for the field ncbiTaxId.
- setNcbiTaxonomyId(Integer) - Method in class net.sourceforge.seqware.webservice.dto.OrganismDto
-
Setter for the field ncbiTaxonomyId.
- setNetwork(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Environment
-
- setNetworkReq(String) - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowInfo
-
Setter for the field networkReq.
- setNewType(String) - Method in class io.seqware.webservice.generated.model.Study
-
- setNewType(String) - Method in class net.sourceforge.seqware.common.model.Study
-
Setter for the field newType.
- SetNodeIdInSession - Class in net.sourceforge.solexatools.util
-
SetNodeIdInSession class.
- SetNodeIdInSession() - Constructor for class net.sourceforge.solexatools.util.SetNodeIdInSession
-
- setNominalLength(Integer) - Method in class io.seqware.webservice.generated.model.ExperimentLibraryDesign
-
- setNominalLength(Integer) - Method in class net.sourceforge.seqware.common.model.ExperimentLibraryDesign
-
Setter for the field nominalLength.
- setNominalSdev(Double) - Method in class io.seqware.webservice.generated.model.ExperimentLibraryDesign
-
- setNominalSdev(Long) - Method in class net.sourceforge.seqware.common.model.ExperimentLibraryDesign
-
Setter for the field nominalSdev.
- setNotes(String) - Method in class io.seqware.webservice.generated.model.Invoice
-
- setNotes(String) - Method in class net.sourceforge.seqware.common.model.Invoice
-
Setter for the field notes.
- setNotRunned(int) - Method in class net.sourceforge.solexatools.webapp.metamodel.StudySampleReportLineItem
-
Setter for the field notRunned.
- setOffspringProcessings(SortedSet<Processing>) - Method in class net.sourceforge.seqware.common.model.WorkflowRun
-
Setter for the field offspringProcessings.
- setOkTo(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object.OozieJob
-
- setOOZIE_APP_PATH(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Environment
-
- setOOZIE_APP_ROOT(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Environment
-
- setOOZIE_JOBTRACKER(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Environment
-
- setOOZIE_NAMENODE(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Environment
-
- setOOZIE_QUEUENAME(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Environment
-
- setOOZIE_URL(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Environment
-
- setOOZIE_WORK_DIR(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Environment
-
- SetOperations - Class in net.sourceforge.seqware.pipeline.tools
-
Taken from http://www.java2s.com/Code/Java/Collections-Data-Structure/Setoperationsunionintersectiondifferencesymmetricdifferenceissubsetissuperset.htm
- SetOperations() - Constructor for class net.sourceforge.seqware.pipeline.tools.SetOperations
-
- setOrganism(String) - Method in class net.sourceforge.seqware.common.model.Lane
-
Setter for the field organism.
- setOrganism(Organism) - Method in class net.sourceforge.seqware.common.model.Sample
-
Setter for the field
organism.
- setOrganism(OrganismDto) - Method in class net.sourceforge.seqware.webservice.dto.LibraryDto
-
Setter for the field organism.
- setOrganismDAO(OrganismDAO) - Method in class net.sourceforge.seqware.common.business.impl.OrganismServiceImpl
-
setOrganismDAO.
- setOrganismDAO(OrganismDAO) - Method in interface net.sourceforge.seqware.common.business.OrganismService
-
setOrganismDAO.
- setOrganismId(Organism) - Method in class io.seqware.webservice.generated.model.Lane
-
- setOrganismId(Integer) - Method in class io.seqware.webservice.generated.model.Organism
-
- setOrganismId(Organism) - Method in class io.seqware.webservice.generated.model.Sample
-
- setOrganismId(Integer) - Method in class net.sourceforge.seqware.common.model.Organism
-
Setter for the field organismId.
- setOrganismId(Integer) - Method in class net.sourceforge.seqware.common.model.Sample
-
Setter for the field
organismId.
- setOrganismId(int) - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.SampleInfo
-
Sets the organismId, as long as the organism id is over 0.
- setOrganismService(OrganismService) - Method in class net.sourceforge.seqware.common.ContextImpl
-
- setOrganismService(OrganismService) - Method in class net.sourceforge.solexatools.webapp.controller.SampleController
-
Setter for the field organismService.
- setOrganismService(OrganismService) - Method in class net.sourceforge.solexatools.webapp.controller.SampleSetupController
-
Setter for the field organismService.
- setOriginalFileName(String) - Method in class net.sourceforge.seqware.common.util.filetools.ProvisionFilesUtil
-
Setter for the field originalFileName.
- setOs(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object.WorkflowExecutable
-
- setOutputDir(String) - Method in class net.sourceforge.seqware.pipeline.bundle.Bundle
-
Setter for the field outputDir.
- setOutputDir(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object.OozieProvisionFileJob
-
- setOutputDir(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object.ProvisionFilesJob
-
- setOutputFiles(Collection<File>) - Method in class net.sourceforge.seqware.common.hibernate.reports.WorkflowRunReportRow
-
Setter for the field outputFiles.
- setOutputLineCapacity(Integer) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Command
-
Set the number of lines of stdout and stderr to output
- setOutputPath(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.SqwFile
-
- setOwner(Registration) - Method in class net.sourceforge.seqware.common.model.Experiment
-
Setter for the field owner.
- setOwner(Registration) - Method in class net.sourceforge.seqware.common.model.File
-
Setter for the field owner.
- setOwner(Registration) - Method in class net.sourceforge.seqware.common.model.Invoice
-
Setter for the field owner.
- setOwner(Registration) - Method in class net.sourceforge.seqware.common.model.IUS
-
Setter for the field owner.
- setOwner(Registration) - Method in class net.sourceforge.seqware.common.model.Lane
-
Setter for the field owner.
- setOwner(Registration) - Method in class net.sourceforge.seqware.common.model.Processing
-
Setter for the field owner.
- setOwner(Registration) - Method in class net.sourceforge.seqware.common.model.Sample
-
Setter for the field
owner.
- setOwner(Registration) - Method in class net.sourceforge.seqware.common.model.SequencerRun
-
Setter for the field owner.
- setOwner(Registration) - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
-
Setter for the field owner.
- setOwner(Registration) - Method in class net.sourceforge.seqware.common.model.Study
-
Setter for the field owner.
- setOwner(Registration) - Method in class net.sourceforge.seqware.common.model.Workflow
-
Setter for the field owner.
- setOwner(Registration) - Method in class net.sourceforge.seqware.common.model.WorkflowRun
-
Setter for the field owner.
- setOwner(OwnerDto) - Method in class net.sourceforge.seqware.webservice.dto.LibraryDto
-
Setter for the field owner.
- setOwnerId(Registration) - Method in class io.seqware.webservice.generated.model.Experiment
-
- setOwnerId(Registration) - Method in class io.seqware.webservice.generated.model.File
-
- setOwnerId(Registration) - Method in class io.seqware.webservice.generated.model.Invoice
-
- setOwnerId(Registration) - Method in class io.seqware.webservice.generated.model.Ius
-
- setOwnerId(Registration) - Method in class io.seqware.webservice.generated.model.Lane
-
- setOwnerId(Registration) - Method in class io.seqware.webservice.generated.model.Processing
-
- setOwnerId(Registration) - Method in class io.seqware.webservice.generated.model.Sample
-
- setOwnerId(Registration) - Method in class io.seqware.webservice.generated.model.SequencerRun
-
- setOwnerId(Registration) - Method in class io.seqware.webservice.generated.model.Study
-
- setOwnerId(Registration) - Method in class io.seqware.webservice.generated.model.Workflow
-
- setOwnerId(Registration) - Method in class io.seqware.webservice.generated.model.WorkflowRun
-
- setOwnerUserName(String) - Method in class net.sourceforge.seqware.common.model.WorkflowRun
-
- setPage(int) - Method in class net.sourceforge.solexatools.webapp.metamodel.Flexigrid
-
Setter for the field page.
- setPaidAmount(BigInteger) - Method in class io.seqware.webservice.generated.model.Invoice
-
- setPaidAmount(Double) - Method in class net.sourceforge.seqware.common.model.Invoice
-
Setter for the field paidAmount.
- setPairedEnd(Boolean) - Method in class io.seqware.webservice.generated.model.SequencerRun
-
- setPairedEnd(Boolean) - Method in class net.sourceforge.seqware.common.model.SequencerRun
-
Setter for the field pairedEnd.
- setPairedEnd(Boolean) - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
-
Setter for the field pairedEnd.
- setPairedEnd(boolean) - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.RunInfo
-
Set the value of pairedEnd
- setPairedEnd(Boolean) - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.SampleInfo
-
- setPairedFilePath(String) - Method in class io.seqware.webservice.generated.model.SequencerRun
-
- setPairedFilePath(String) - Method in class net.sourceforge.seqware.common.model.SequencerRun
-
Setter for the field pairedFilePath.
- setPairedFilePath(String) - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
-
Setter for the field pairedFilePath.
- setPairedOrientation(String) - Method in class io.seqware.webservice.generated.model.ExperimentLibraryDesign
-
- setPairedOrientation(String) - Method in class net.sourceforge.seqware.common.model.ExperimentLibraryDesign
-
Setter for the field pairedOrientation.
- setParameters(String) - Method in class io.seqware.webservice.generated.model.Processing
-
- setParameters(String) - Method in class net.sourceforge.seqware.common.model.Processing
-
Setter for the field parameters.
- setParameters(String) - Method in class net.sourceforge.seqware.common.module.ReturnValue
-
Setter for the field parameters.
- setParameters(List<String>) - Method in class net.sourceforge.seqware.pipeline.module.Module
-
setParameters.
- setParameters(List<String>) - Method in interface net.sourceforge.seqware.pipeline.module.ModuleInterface
-
setParameters.
- setParams(List<String>) - Method in interface net.sourceforge.seqware.pipeline.decider.DeciderInterface
-
Lets you set a List of params so the plugin can deal with parameters
- setParams(List<String>) - Method in class net.sourceforge.seqware.pipeline.plugin.Plugin
-
Lets you set a List of params so the plugin can deal with parameters
- setParams(List<String>) - Method in interface net.sourceforge.seqware.pipeline.plugin.PluginInterface
-
Lets you set a List of params so the plugin can deal with parameters
- setParams(List<String>) - Method in class net.sourceforge.seqware.pipeline.plugins.HelloWorld
-
Lets you set a List of params so the plugin can deal with parameters
- setParams(List<String>) - Method in class net.sourceforge.seqware.pipeline.plugins.MarkdownPlugin
-
Lets you set a List of params so the plugin can deal with parameters
- setParams(List<String>) - Method in class net.sourceforge.seqware.pipeline.plugins.WorkflowRunFilesInitialPopulationPlugin
-
Lets you set a List of params so the plugin can deal with parameters
- setParams(SortedSet<WorkflowParam>) - Method in class net.sourceforge.solexatools.util.SummaryLine
-
Setter for the field params.
- setParentAccessions(Collection<String>) - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object.OozieJob
-
- setParentAccessions(Collection<String>) - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object.PegasusJob
-
- setParentAccessions(Collection<String>) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.AbstractJob
-
- setParentAccessions(Collection<String>) - Method in interface net.sourceforge.seqware.pipeline.workflowV2.model.Job
-
set parent accessiosns for the job
- setParentAccessions(Collection<String>) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.JobBatch
-
- setParentAccessions(Collection<String>) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.SqwFile
-
set the parent accessions for provision file job
- setParentId(Processing) - Method in class io.seqware.webservice.generated.model.ProcessingRelationship
-
- setParentId(Sample) - Method in class io.seqware.webservice.generated.model.SampleRelationship
-
- setParentId(int) - Method in class net.sourceforge.seqware.queryengine.webservice.model.SampleHierarchy
-
- setParentProcessingAccession(Integer) - Method in class io.seqware.webservice.generated.model.WorkflowRunParam
-
- setParentProcessingAccession(Integer) - Method in class net.sourceforge.seqware.common.model.WorkflowRunParam
-
Setter for the field parentProcessingAccession.
- setParentProcessings(Collection<Processing>) - Method in class net.sourceforge.seqware.common.hibernate.reports.WorkflowRunReportRow
-
Setter for the field parentProcessings.
- setParents(Set<Processing>) - Method in class net.sourceforge.seqware.common.model.Processing
-
Setter for the field parents.
- setParents(Set<Sample>) - Method in class net.sourceforge.seqware.common.model.Sample
-
Setter for the field
parents.
- setParents(Collection<Job>) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.AbstractJob
-
set parent jobs
- setParentUrls(Set<String>) - Method in class net.sourceforge.seqware.webservice.dto.LibraryDto
-
Setter for the field parentUrls.
- setParentWorkflowAccessions(Set<String>) - Method in class net.sourceforge.seqware.pipeline.deciders.BasicDecider
-
- setPassword(String) - Method in class io.seqware.webservice.generated.model.Registration
-
- setPassword(String) - Method in class net.sourceforge.seqware.common.model.Registration
-
Setter for the field password.
- setPasswordHint(String) - Method in class io.seqware.webservice.generated.model.Registration
-
- setPasswordHint(String) - Method in class net.sourceforge.seqware.common.model.Registration
-
Setter for the field passwordHint.
- setPathToFirstFile(String) - Method in class net.sourceforge.seqware.common.model.UploadSequence
-
Setter for the field pathToFirstFile.
- setPathToSecondFile(String) - Method in class net.sourceforge.seqware.common.model.UploadSequence
-
Setter for the field pathToSecondFile.
- setPayee(boolean) - Method in class io.seqware.webservice.generated.model.Registration
-
- setPayee(boolean) - Method in class net.sourceforge.seqware.common.model.Registration
-
Setter for the field payee.
- setPeakMemory(int) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Environment
-
set the max memory for the workflow
- setPeakThreads(int) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Environment
-
set the max threads for the workflow
- setPegasusConfigDir(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Environment
-
- setPending(int) - Method in class net.sourceforge.solexatools.webapp.metamodel.StudySampleReportLineItem
-
Setter for the field pending.
- setPermanentBundleLocation(String) - Method in class io.seqware.webservice.generated.model.Workflow
-
- setPermanentBundleLocation(String) - Method in class net.sourceforge.seqware.common.model.Workflow
-
Setter for the field permanentBundleLocation.
- setPermBundleLocation(String) - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowInfo
-
Setter for the field permBundleLocation.
- setPfn(Pfn) - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object.WorkflowExecutable
-
- setPlatform(Platform) - Method in class net.sourceforge.seqware.common.model.Experiment
-
Setter for the field platform.
- setPlatform(Platform) - Method in class net.sourceforge.seqware.common.model.SequencerRun
-
Setter for the field platform.
- setPlatform(Platform) - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
-
Setter for the field platform.
- setPlatformDAO(PlatformDAO) - Method in class net.sourceforge.seqware.common.business.impl.PlatformServiceImpl
-
setPlatformDAO.
- setPlatformDAO(PlatformDAO) - Method in interface net.sourceforge.seqware.common.business.PlatformService
-
setPlatformDAO.
- setPlatformId(Platform) - Method in class io.seqware.webservice.generated.model.Experiment
-
- setPlatformId(Integer) - Method in class io.seqware.webservice.generated.model.Platform
-
- setPlatformId(Platform) - Method in class io.seqware.webservice.generated.model.SequencerRun
-
- setPlatformId(Integer) - Method in class net.sourceforge.seqware.common.model.Platform
-
Setter for the field platformId.
- setPlatformId(int) - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.RunInfo
-
- setPlatformInt(Integer) - Method in class net.sourceforge.seqware.common.model.Experiment
-
Setter for the field platformInt.
- setPlatformInt(int) - Method in class net.sourceforge.seqware.common.model.SequencerRun
-
Setter for the field platformInt.
- setPlatformService(PlatformService) - Method in class net.sourceforge.seqware.common.ContextImpl
-
Setter for the field platformService.
- setPlatformService(PlatformService) - Method in class net.sourceforge.solexatools.webapp.controller.ExperimentController
-
Setter for the field platformService.
- setPlatformService(PlatformService) - Method in class net.sourceforge.solexatools.webapp.controller.ExperimentSetupController
-
Setter for the field platformService.
- setPlatformService(PlatformService) - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunWizardController
-
Setter for the field platformService.
- setPlatformService(PlatformService) - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunWizardSetupController
-
Setter for the field platformService.
- setPricePerUnit(BigInteger) - Method in class io.seqware.webservice.generated.model.Expense
-
- setPricePerUnit(Double) - Method in class net.sourceforge.seqware.common.model.Expense
-
Setter for the field
pricePerUnit.
- setPrivate(boolean) - Method in class net.sourceforge.seqware.common.model.Workflow
-
setPrivate.
- setProcCountInfo(List<SequencerRun>) - Method in class net.sourceforge.seqware.common.business.impl.SequencerRunServiceImpl
-
setProcCountInfo.
- setProcCountInfo(List<SequencerRun>) - Method in interface net.sourceforge.seqware.common.business.SequencerRunService
-
setProcCountInfo.
- setProcess(Boolean) - Method in class io.seqware.webservice.generated.model.SequencerRun
-
- setProcess(Boolean) - Method in class net.sourceforge.seqware.common.model.SequencerRun
-
Setter for the field process.
- setProcessedCount(Integer) - Method in class net.sourceforge.seqware.common.model.SequencerRun
-
Setter for the field processedCount.
- setProcessExitStatus(Integer) - Method in class io.seqware.webservice.generated.model.Processing
-
- setProcessExitStatus(Integer) - Method in class net.sourceforge.seqware.common.model.Processing
-
Setter for the field processExitStatus.
- setProcessExitStatus(int) - Method in class net.sourceforge.seqware.common.module.ReturnValue
-
Setter for the field processExitStatus.
- setProcessing(Processing) - Method in class net.sourceforge.seqware.common.model.FileReportRow
-
Setter for the field processing.
- setProcessing(Processing) - Method in class net.sourceforge.seqware.common.model.ProcessingAttribute
-
Setter for the field processing.
- setProcessing(Processing) - Method in class net.sourceforge.seqware.common.model.ProcessingExperiments
-
Setter for the field processing.
- setProcessing(Processing) - Method in class net.sourceforge.seqware.common.model.ProcessingIus
-
Setter for the field processing.
- setProcessing(Processing) - Method in class net.sourceforge.seqware.common.model.ProcessingLanes
-
Setter for the field processing.
- setProcessing(Processing) - Method in class net.sourceforge.seqware.common.model.ProcessingSamples
-
Setter for the field processing.
- setProcessing(Processing) - Method in class net.sourceforge.seqware.common.model.ProcessingSequencerRuns
-
Setter for the field processing.
- setProcessing(Processing) - Method in class net.sourceforge.seqware.common.model.ProcessingStudies
-
Setter for the field processing.
- setProcessing(Processing) - Method in class net.sourceforge.seqware.common.model.ShareProcessing
-
Setter for the field processing.
- setProcessingAccession(int) - Method in class net.sourceforge.seqware.pipeline.module.Module
-
Setter for the field processingAccession.
- setProcessingAttributeCollection(Collection<ProcessingAttribute>) - Method in class io.seqware.webservice.generated.model.Processing
-
- setProcessingAttributeId(Integer) - Method in class io.seqware.webservice.generated.model.ProcessingAttribute
-
- setProcessingAttributeId(int) - Method in class net.sourceforge.seqware.common.model.ProcessingAttribute
-
Setter for the field processingAttributeId.
- setProcessingAttributes(Set<ProcessingAttribute>) - Method in class net.sourceforge.seqware.common.model.Processing
-
Setter for the field processingAttributes.
- setProcessingByChildId(Processing) - Method in class net.sourceforge.seqware.common.model.ProcessingRelationship
-
Setter for the field processingByChildId.
- setProcessingByParentId(Processing) - Method in class net.sourceforge.seqware.common.model.ProcessingRelationship
-
Setter for the field processingByParentId.
- setProcessingCollection(Collection<Processing>) - Method in class io.seqware.webservice.generated.model.Registration
-
- setProcessingCollection(Collection<Processing>) - Method in class io.seqware.webservice.generated.model.WorkflowRun
-
- setProcessingCollection1(Collection<Processing>) - Method in class io.seqware.webservice.generated.model.WorkflowRun
-
- setProcessingCount(Integer) - Method in class net.sourceforge.seqware.common.model.SequencerRun
-
Setter for the field processingCount.
- setProcessingDAO(ProcessingDAO) - Method in class net.sourceforge.seqware.common.business.impl.FileUploadServiceImpl
-
Setter for the field processingDAO.
- setProcessingDAO(ProcessingDAO) - Method in class net.sourceforge.seqware.common.business.impl.LaneServiceImpl
-
Sets a private member variable with an instance of an implementation of
ProcessingDAO.
- setProcessingDAO(ProcessingDAO) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingServiceImpl
-
setProcessingDAO.
- setProcessingDAO(ProcessingDAO) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowRunServiceImpl
-
Setter for the field processingDAO.
- setProcessingDAO(ProcessingDAO) - Method in interface net.sourceforge.seqware.common.business.ProcessingService
-
setProcessingDAO.
- setProcessingExperimentsCollection(Collection<ProcessingExperiments>) - Method in class io.seqware.webservice.generated.model.Experiment
-
- setProcessingExperimentsCollection(Collection<ProcessingExperiments>) - Method in class io.seqware.webservice.generated.model.Processing
-
- setProcessingExperimentsDAO(ProcessingExperimentsDAO) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingExperimentsServiceImpl
-
setProcessingExperimentsDAO.
- setProcessingExperimentsDAO(ProcessingExperimentsDAO) - Method in interface net.sourceforge.seqware.common.business.ProcessingExperimentsService
-
setProcessingExperimentsDAO.
- setProcessingExperimentsId(Integer) - Method in class io.seqware.webservice.generated.model.ProcessingExperiments
-
- setProcessingExperimentsId(int) - Method in class net.sourceforge.seqware.common.model.ProcessingExperiments
-
Setter for the field processingExperimentsId.
- setProcessingExperimentsService(ProcessingExperimentsService) - Method in class net.sourceforge.seqware.common.ContextImpl
-
Setter for the field processingExperimentsService.
- setProcessingFilesCollection(Collection<ProcessingFiles>) - Method in class io.seqware.webservice.generated.model.File
-
- setProcessingFilesCollection(Collection<ProcessingFiles>) - Method in class io.seqware.webservice.generated.model.Processing
-
- setProcessingFilesId(Integer) - Method in class io.seqware.webservice.generated.model.ProcessingFiles
-
- setProcessingForSequrncerRun(Processing, HttpServletRequest) - Static method in class net.sourceforge.solexatools.util.SetNodeIdInSession
-
setProcessingForSequrncerRun.
- setProcessingForStudy(Processing, HttpServletRequest) - Static method in class net.sourceforge.solexatools.util.SetNodeIdInSession
-
setProcessingForStudy.
- setProcessingForWorkflowRun(Processing, HttpServletRequest) - Static method in class net.sourceforge.solexatools.util.SetNodeIdInSession
-
setProcessingForWorkflowRun.
- setProcessingForWorkflowRunRunning(Processing, HttpServletRequest) - Static method in class net.sourceforge.solexatools.util.SetNodeIdInSession
-
setProcessingForWorkflowRunRunning.
- setProcessingId(Integer) - Method in class io.seqware.webservice.generated.model.FileReport
-
- setProcessingId(Integer) - Method in class io.seqware.webservice.generated.model.Processing
-
- setProcessingId(Processing) - Method in class io.seqware.webservice.generated.model.ProcessingAttribute
-
- setProcessingId(Processing) - Method in class io.seqware.webservice.generated.model.ProcessingExperiments
-
- setProcessingId(Processing) - Method in class io.seqware.webservice.generated.model.ProcessingFiles
-
- setProcessingId(Processing) - Method in class io.seqware.webservice.generated.model.ProcessingIus
-
- setProcessingId(Processing) - Method in class io.seqware.webservice.generated.model.ProcessingLanes
-
- setProcessingId(Processing) - Method in class io.seqware.webservice.generated.model.ProcessingSamples
-
- setProcessingId(Processing) - Method in class io.seqware.webservice.generated.model.ProcessingSequencerRuns
-
- setProcessingId(Processing) - Method in class io.seqware.webservice.generated.model.ProcessingStudies
-
- setProcessingId(Processing) - Method in class io.seqware.webservice.generated.model.ShareProcessing
-
- setProcessingId(Integer) - Method in class net.sourceforge.seqware.common.model.Processing
-
Setter for the field processingId.
- setProcessingIusCollection(Collection<ProcessingIus>) - Method in class io.seqware.webservice.generated.model.Ius
-
- setProcessingIusCollection(Collection<ProcessingIus>) - Method in class io.seqware.webservice.generated.model.Processing
-
- setProcessingIUSDAO(ProcessingIUSDAO) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingIUSServiceImpl
-
setProcessingIUSDAO.
- setProcessingIUSDAO(ProcessingIUSDAO) - Method in interface net.sourceforge.seqware.common.business.ProcessingIUSService
-
setProcessingIUSDAO.
- setProcessingIusId(Integer) - Method in class io.seqware.webservice.generated.model.ProcessingIus
-
- setProcessingIusId(int) - Method in class net.sourceforge.seqware.common.model.ProcessingIus
-
Setter for the field processingIusId.
- setProcessingIusService(ProcessingIUSService) - Method in class net.sourceforge.seqware.common.ContextImpl
-
Setter for the field processingIusService.
- setProcessingLanesCollection(Collection<ProcessingLanes>) - Method in class io.seqware.webservice.generated.model.Lane
-
- setProcessingLanesCollection(Collection<ProcessingLanes>) - Method in class io.seqware.webservice.generated.model.Processing
-
- setProcessingLanesDAO(ProcessingLanesDAO) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingLanesServiceImpl
-
setProcessingLanesDAO.
- setProcessingLanesDAO(ProcessingLanesDAO) - Method in interface net.sourceforge.seqware.common.business.ProcessingLanesService
-
setProcessingLanesDAO.
- setProcessingLaneService(ProcessingLanesService) - Method in class net.sourceforge.seqware.common.ContextImpl
-
Setter for the field processingLaneService.
- setProcessingLanesId(Integer) - Method in class io.seqware.webservice.generated.model.ProcessingLanes
-
- setProcessingLanesId(int) - Method in class net.sourceforge.seqware.common.model.ProcessingLanes
-
Setter for the field processingLanesId.
- setProcessingRelationshipCollection(Collection<ProcessingRelationship>) - Method in class io.seqware.webservice.generated.model.Processing
-
- setProcessingRelationshipCollection1(Collection<ProcessingRelationship>) - Method in class io.seqware.webservice.generated.model.Processing
-
- setProcessingRelationshipDAO(ProcessingRelationshipDAO) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingRelationshipServiceImpl
-
setProcessingRelationshipDAO.
- setProcessingRelationshipDAO(ProcessingRelationshipDAO) - Method in interface net.sourceforge.seqware.common.business.ProcessingRelationshipService
-
setProcessingRelationshipDAO.
- setProcessingRelationshipId(Integer) - Method in class io.seqware.webservice.generated.model.ProcessingRelationship
-
- setProcessingRelationshipId(int) - Method in class net.sourceforge.seqware.common.model.ProcessingRelationship
-
Setter for the field processingRelationshipId.
- setProcessingRelationshipService(ProcessingRelationshipService) - Method in class net.sourceforge.seqware.common.ContextImpl
-
Setter for the field processingRelationshipService.
- setProcessings(Set<Processing>) - Method in class net.sourceforge.seqware.common.model.Experiment
-
Setter for the field processings.
- setProcessings(Set<Processing>) - Method in class net.sourceforge.seqware.common.model.File
-
Setter for the field processings.
- setProcessings(Set<Processing>) - Method in class net.sourceforge.seqware.common.model.IUS
-
Setter for the field processings.
- setProcessings(Set<Processing>) - Method in class net.sourceforge.seqware.common.model.Lane
-
Setter for the field processings.
- setProcessings(Set<Processing>) - Method in class net.sourceforge.seqware.common.model.Sample
-
Setter for the field
processings.
- setProcessings(Set<Processing>) - Method in class net.sourceforge.seqware.common.model.SequencerRun
-
Setter for the field processings.
- setProcessings(SortedSet<Processing>) - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
-
Setter for the field processings.
- setProcessings(Set<Processing>) - Method in class net.sourceforge.seqware.common.model.Study
-
Setter for the field processings.
- setProcessings(SortedSet<Processing>) - Method in class net.sourceforge.seqware.common.model.WorkflowRun
-
Setter for the field processings.
- setProcessingSamplesCollection(Collection<ProcessingSamples>) - Method in class io.seqware.webservice.generated.model.Processing
-
- setProcessingSamplesCollection(Collection<ProcessingSamples>) - Method in class io.seqware.webservice.generated.model.Sample
-
- setProcessingSamplesDAO(ProcessingSamplesDAO) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingSamplesServiceImpl
-
setProcessingSamplesDAO.
- setProcessingSamplesDAO(ProcessingSamplesDAO) - Method in interface net.sourceforge.seqware.common.business.ProcessingSamplesService
-
setProcessingSamplesDAO.
- setProcessingSamplesId(Integer) - Method in class io.seqware.webservice.generated.model.ProcessingSamples
-
- setProcessingSamplesId(int) - Method in class net.sourceforge.seqware.common.model.ProcessingSamples
-
Setter for the field processingSamplesId.
- setProcessingSamplesService(ProcessingSamplesService) - Method in class net.sourceforge.seqware.common.ContextImpl
-
Setter for the field processingSamplesService.
- setProcessingSequencerRunsCollection(Collection<ProcessingSequencerRuns>) - Method in class io.seqware.webservice.generated.model.Processing
-
- setProcessingSequencerRunsCollection(Collection<ProcessingSequencerRuns>) - Method in class io.seqware.webservice.generated.model.SequencerRun
-
- setProcessingSequencerRunsDAO(ProcessingSequencerRunsDAO) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingSequencerRunsServiceImpl
-
setProcessingSequencerRunsDAO.
- setProcessingSequencerRunsDAO(ProcessingSequencerRunsDAO) - Method in interface net.sourceforge.seqware.common.business.ProcessingSequencerRunsService
-
setProcessingSequencerRunsDAO.
- setProcessingSequencerRunService(ProcessingSequencerRunsService) - Method in class net.sourceforge.seqware.common.ContextImpl
-
Setter for the field processingSequencerRunService.
- setProcessingSequencerRunsId(Integer) - Method in class io.seqware.webservice.generated.model.ProcessingSequencerRuns
-
- setProcessingSequencerRunsId(int) - Method in class net.sourceforge.seqware.common.model.ProcessingSequencerRuns
-
Setter for the field processingSequencerRunsId.
- setProcessingService(ProcessingService) - Method in class net.sourceforge.seqware.common.ContextImpl
-
Setter for the field processingService.
- setProcessingService(ProcessingService) - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysBulkDownloadListDetailsController
-
Setter for the field processingService.
- setProcessingService(ProcessingService) - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysListDetailsController
-
Setter for the field processingService.
- setProcessingService(ProcessingService) - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysRunningListDetailsController
-
Setter for the field processingService.
- setProcessingService(ProcessingService) - Method in class net.sourceforge.solexatools.webapp.controller.BulkDownloadListDetailsController
-
Setter for the field processingService.
- setProcessingService(ProcessingService) - Method in class net.sourceforge.solexatools.webapp.controller.DownloadFileListController
-
Setter for the field processingService.
- setProcessingService(ProcessingService) - Method in class net.sourceforge.solexatools.webapp.controller.EntityController
-
Setter for the field processingService.
- setProcessingService(ProcessingService) - Method in class net.sourceforge.solexatools.webapp.controller.LaunchWorkflowListDetailsController
-
Setter for the field processingService.
- setProcessingService(ProcessingService) - Method in class net.sourceforge.solexatools.webapp.controller.ProcessingController
-
Setter for the field processingService.
- setProcessingService(ProcessingService) - Method in class net.sourceforge.solexatools.webapp.controller.ProcessingSetupController
-
Setter for the field processingService.
- setProcessingService(ProcessingService) - Method in class net.sourceforge.solexatools.webapp.controller.SaveOpenNodeController
-
Setter for the field processingService.
- setProcessingService(ProcessingService) - Method in class net.sourceforge.solexatools.webapp.controller.SearchResultsListController
-
Setter for the field processingService.
- setProcessingService(ProcessingService) - Method in class net.sourceforge.solexatools.webapp.controller.SelectInputListController
-
Setter for the field processingService.
- setProcessingService(ProcessingService) - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunListDetailsController
-
Setter for the field processingService.
- setProcessingService(ProcessingService) - Method in class net.sourceforge.solexatools.webapp.controller.StudyListDetailsController
-
Setter for the field processingService.
- setProcessingService(ProcessingService) - Method in class net.sourceforge.solexatools.webapp.controller.StudyListDetailsFlatController
-
Setter for the field processingService.
- setProcessingService(ProcessingService) - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileController
-
Setter for the field processingService.
- setProcessingService(ProcessingService) - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileSetupController
-
Setter for the field processingService.
- setProcessingService(ProcessingService) - Method in class net.sourceforge.solexatools.webapp.controller.UploadSequenceController
-
Setter for the field processingService.
- setProcessingsForView(Set<Processing>) - Method in class net.sourceforge.seqware.common.model.Lane
-
setProcessingsForView.
- setProcessingStudiesCollection(Collection<ProcessingStudies>) - Method in class io.seqware.webservice.generated.model.Processing
-
- setProcessingStudiesCollection(Collection<ProcessingStudies>) - Method in class io.seqware.webservice.generated.model.Study
-
- setProcessingStudiesDAO(ProcessingStudiesDAO) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingStudiesServiceImpl
-
setProcessingStudiesDAO.
- setProcessingStudiesDAO(ProcessingStudiesDAO) - Method in interface net.sourceforge.seqware.common.business.ProcessingStudiesService
-
setProcessingStudiesDAO.
- setProcessingStudiesId(Integer) - Method in class io.seqware.webservice.generated.model.ProcessingStudies
-
- setProcessingStudiesId(int) - Method in class net.sourceforge.seqware.common.model.ProcessingStudies
-
Setter for the field processingStudiesId.
- setProcessingStudiesService(ProcessingStudiesService) - Method in class net.sourceforge.seqware.common.ContextImpl
-
Setter for the field processingStudiesService.
- setProjectCode(String) - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.SampleInfo
-
- setProjectId(int) - Method in class io.seqware.webservice.generated.model.Study
-
- setProjectId(Integer) - Method in class net.sourceforge.seqware.common.model.Study
-
Setter for the field projectId.
- setPublic(boolean) - Method in class net.sourceforge.seqware.common.model.Workflow
-
setPublic.
- setQsubOptions(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.AbstractJob
-
Allows specifying options to qsub.
- setQualityMultiplier(Integer) - Method in class io.seqware.webservice.generated.model.Experiment
-
- setQualityMultiplier(Integer) - Method in class net.sourceforge.seqware.common.model.Experiment
-
Setter for the field qualityMultiplier.
- setQualityNumberOfLevels(Integer) - Method in class io.seqware.webservice.generated.model.Experiment
-
- setQualityNumberOfLevels(Integer) - Method in class net.sourceforge.seqware.common.model.Experiment
-
Setter for the field qualityNumberOfLevels.
- setQualityScorer(String) - Method in class io.seqware.webservice.generated.model.Experiment
-
- setQualityScorer(String) - Method in class io.seqware.webservice.generated.model.SequencerRun
-
- setQualityScorer(String) - Method in class net.sourceforge.seqware.common.model.Experiment
-
Setter for the field qualityScorer.
- setQualityType(String) - Method in class io.seqware.webservice.generated.model.Experiment
-
- setQualityType(String) - Method in class net.sourceforge.seqware.common.model.Experiment
-
Setter for the field qualityType.
- setQueue(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.AbstractJob
-
- setQueue(String) - Method in interface net.sourceforge.seqware.pipeline.workflowV2.model.Job
-
set the queue
- setQueue(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.JobBatch
-
- setRandom(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.AbstractWorkflowDataModel
-
set the pre-defined random variable
- setReadClass(String) - Method in class io.seqware.webservice.generated.model.ExperimentSpotDesignReadSpec
-
- setReadClass(String) - Method in class net.sourceforge.seqware.common.model.ExperimentSpotDesignReadSpec
-
Setter for the field readClass.
- setReader(BufferedReader) - Method in class net.sourceforge.seqware.common.util.iotools.BufferedReaderThread
-
Setter for the field reader.
- setReadIndex(Integer) - Method in class io.seqware.webservice.generated.model.ExperimentSpotDesignReadSpec
-
- setReadIndex(Integer) - Method in class net.sourceforge.seqware.common.model.ExperimentSpotDesignReadSpec
-
Setter for the field readIndex.
- setReadLabel(String) - Method in class io.seqware.webservice.generated.model.ExperimentSpotDesignReadSpec
-
- setReadLabel(String) - Method in class net.sourceforge.seqware.common.model.ExperimentSpotDesignReadSpec
-
Setter for the field readLabel.
- setReadSpec(String) - Method in class io.seqware.webservice.generated.model.ExperimentSpotDesign
-
- setReadSpec(String) - Method in class net.sourceforge.seqware.common.model.ExperimentSpotDesign
-
Setter for the field readSpec.
- setReadSpecs(SortedSet<ExperimentSpotDesignReadSpec>) - Method in class net.sourceforge.seqware.common.model.ExperimentSpotDesign
-
Setter for the field readSpecs.
- setReadsPerSpot(Integer) - Method in class io.seqware.webservice.generated.model.ExperimentSpotDesign
-
- setReadsPerSpot(Integer) - Method in class net.sourceforge.seqware.common.model.ExperimentSpotDesign
-
Setter for the field readsPerSpot.
- setReadType(String) - Method in class io.seqware.webservice.generated.model.ExperimentSpotDesignReadSpec
-
- setReadType(String) - Method in class net.sourceforge.seqware.common.model.ExperimentSpotDesignReadSpec
-
Setter for the field readType.
- setReadyToProcess(String) - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
-
Setter for the field readyToProcess.
- setRefLane(Integer) - Method in class io.seqware.webservice.generated.model.SequencerRun
-
- setRefLane(Integer) - Method in class net.sourceforge.seqware.common.model.SequencerRun
-
Setter for the field refLane.
- setRefLane(Integer) - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
-
Setter for the field refLane.
- setRegions(String) - Method in class io.seqware.webservice.generated.model.Lane
-
- setRegions(String) - Method in class io.seqware.webservice.generated.model.Sample
-
- setRegions(String) - Method in class net.sourceforge.seqware.common.model.Lane
-
Setter for the field regions.
- setRegions(String) - Method in class net.sourceforge.seqware.common.model.Sample
-
Setter for the field
regions.
- setRegistration(Registration) - Method in class net.sourceforge.seqware.common.model.ShareExperiment
-
Setter for the field registration.
- setRegistration(Registration) - Method in class net.sourceforge.seqware.common.model.ShareFile
-
Setter for the field registration.
- setRegistration(Registration) - Method in class net.sourceforge.seqware.common.model.ShareLane
-
Setter for the field registration.
- setRegistration(Registration) - Method in class net.sourceforge.seqware.common.model.ShareProcessing
-
Setter for the field registration.
- setRegistration(Registration) - Method in class net.sourceforge.seqware.common.model.ShareSample
-
Setter for the field registration.
- setRegistration(Registration) - Method in class net.sourceforge.seqware.common.model.ShareStudy
-
Setter for the field registration.
- setRegistration(Registration) - Method in class net.sourceforge.seqware.common.model.ShareWorkflowRun
-
Setter for the field registration.
- setRegistrationDAO(RegistrationDAO) - Method in class net.sourceforge.seqware.common.business.impl.RegistrationServiceImpl
-
setRegistrationDAO.
- setRegistrationDAO(RegistrationDAO) - Method in interface net.sourceforge.seqware.common.business.RegistrationService
-
setRegistrationDAO.
- setRegistrationId(Integer) - Method in class io.seqware.webservice.generated.model.Registration
-
- setRegistrationId(Registration) - Method in class io.seqware.webservice.generated.model.ShareExperiment
-
- setRegistrationId(Registration) - Method in class io.seqware.webservice.generated.model.ShareFile
-
- setRegistrationId(Registration) - Method in class io.seqware.webservice.generated.model.ShareLane
-
- setRegistrationId(Registration) - Method in class io.seqware.webservice.generated.model.ShareProcessing
-
- setRegistrationId(Registration) - Method in class io.seqware.webservice.generated.model.ShareSample
-
- setRegistrationId(Registration) - Method in class io.seqware.webservice.generated.model.ShareStudy
-
- setRegistrationId(Registration) - Method in class io.seqware.webservice.generated.model.ShareWorkflowRun
-
- setRegistrationId(Integer) - Method in class net.sourceforge.seqware.common.model.Registration
-
Setter for the field registrationId.
- setRegistrationService(RegistrationService) - Method in class net.sourceforge.seqware.common.ContextImpl
-
Setter for the field registrationService.
- setRegistrationService(RegistrationService) - Static method in class net.sourceforge.seqware.webservice.resources.BasicResource
-
Setter for the field registrationService.
- setRegistrationService(RegistrationService) - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysEventController
-
Setter for the field registrationService.
- setRegistrationService(RegistrationService) - Method in class net.sourceforge.solexatools.webapp.controller.InviteNewUserController
-
Setter for the field registrationService.
- setRegistrationService(RegistrationService) - Method in class net.sourceforge.solexatools.webapp.controller.InviteNewUserValidatorController
-
Setter for the field registrationService.
- setRegistrationService(RegistrationService) - Method in class net.sourceforge.solexatools.webapp.controller.LoginController
-
Setter for the field registrationService.
- setRegistrationService(RegistrationService) - Method in class net.sourceforge.solexatools.webapp.controller.RegistrationController
-
Setter for the field registrationService.
- setRegistrationService(RegistrationService) - Method in class net.sourceforge.solexatools.webapp.controller.RegistrationSetupController
-
Setter for the field registrationService.
- setRegistrationService(RegistrationService) - Method in class net.sourceforge.solexatools.webapp.controller.ShareValidatorController
-
Setter for the field registrationService.
- setRegistrationService(RegistrationService) - Method in class net.sourceforge.solexatools.webapp.controller.SignUpController
-
Setter for the field registrationService.
- setRegistrationService(RegistrationService) - Method in class net.sourceforge.solexatools.webapp.controller.StudyController
-
Setter for the field registrationService.
- setRelationship(String) - Method in class io.seqware.webservice.generated.model.ProcessingRelationship
-
- setRelationship(String) - Method in class io.seqware.webservice.generated.model.SampleRelationship
-
- setRelationship(String) - Method in class net.sourceforge.seqware.common.model.ProcessingRelationship
-
Setter for the field relationship.
- setReportInputFiles(boolean) - Method in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles
-
- setRequireFiles(boolean) - Method in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles
-
Setter for the field requireFiles.
- setRequirements(Collection<Requirement>) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.AbstractJob
-
- setReturnValue(ReturnValue) - Method in exception net.sourceforge.seqware.common.err.OldSeqwareException
-
Setter for the field returnValue.
- setReturnValue(int) - Method in class net.sourceforge.seqware.common.module.ReturnValue
-
Setter for the field returnValue.
- setRootProcessingName(String) - Method in class net.sourceforge.seqware.common.business.impl.ValidationReportServiceImpl.ReportEntry
-
- setRootProcessingSwa(String) - Method in class net.sourceforge.seqware.common.business.impl.ValidationReportServiceImpl.ReportEntry
-
- setRootSample(Sample) - Method in class net.sourceforge.solexatools.webapp.metamodel.StudySampleReportFileLineItem
-
Setter for the field rootSample.
- setRowId(Integer) - Method in class io.seqware.webservice.generated.model.FileReport
-
- setRowId(Integer) - Method in class io.seqware.webservice.generated.model.SampleReport
-
- setRowId(Integer) - Method in class net.sourceforge.seqware.common.model.FileReportRow
-
Setter for the field rowId.
- setRowId(Integer) - Method in class net.sourceforge.seqware.common.model.SampleReportRow
-
Setter for the field rowId.
- setRows(List<Flexigrid.Cells>) - Method in class net.sourceforge.solexatools.webapp.metamodel.Flexigrid
-
Setter for the field rows.
- setRunAttribute(String, String) - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.RunInfo
-
Adds a new run attribute if the tag does not exist for this run, or changes the value of an existing run attribute.
- setRunAttributes(Set<TagValueUnit>) - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.RunInfo
-
Set the value of runAttributes
- setRunCenter(String) - Method in class io.seqware.webservice.generated.model.SequencerRun
-
- setRunCenter(String) - Method in class net.sourceforge.seqware.common.model.SequencerRun
-
Setter for the field runCenter.
- setRunCenter(String) - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
-
Setter for the field runCenter.
- setRunDescription(String) - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.RunInfo
-
Set the value of runDescription
- setRunFilePath(String) - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.RunInfo
-
Set the value of runFilePath
- setRunName(String) - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.RunInfo
-
Set the value of runName
- setRunSkip(boolean) - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.RunInfo
-
Set the value of runSkip
- setRunStartTimestamp(Date) - Method in class net.sourceforge.seqware.common.model.Processing
-
Setter for the field runStartTimestamp.
- setRunStartTstmp(Date) - Method in class io.seqware.webservice.generated.model.Processing
-
- setRunStartTstmp(Date) - Method in class net.sourceforge.seqware.common.module.ReturnValue
-
Setter for the field runStartTstmp.
- setRunStopTimestamp(Date) - Method in class net.sourceforge.seqware.common.model.Processing
-
Setter for the field runStopTimestamp.
- setRunStopTstmp(Date) - Method in class io.seqware.webservice.generated.model.Processing
-
- setRunStopTstmp(Date) - Method in class net.sourceforge.seqware.common.module.ReturnValue
-
Setter for the field runStopTstmp.
- setSample(Sample) - Method in class net.sourceforge.seqware.common.model.FileReportRow
-
Setter for the field sample.
- setSample(Sample) - Method in class net.sourceforge.seqware.common.model.IUS
-
Setter for the field sample.
- setSample(Sample) - Method in class net.sourceforge.seqware.common.model.Lane
-
Setter for the field sample.
- setSample(Sample) - Method in class net.sourceforge.seqware.common.model.ProcessingSamples
-
Setter for the field sample.
- setSample(Sample) - Method in class net.sourceforge.seqware.common.model.SampleAttribute
-
Setter for the field sample.
- setSample(Sample) - Method in class net.sourceforge.seqware.common.model.SampleLink
-
Setter for the field sample.
- setSample(Sample) - Method in class net.sourceforge.seqware.common.model.SampleSearch
-
Setter for the field sample.
- setSample(Sample) - Method in class net.sourceforge.seqware.common.model.ShareSample
-
Setter for the field sample.
- setSample(Sample) - Method in class net.sourceforge.seqware.common.model.UploadSequence
-
Setter for the field sample.
- setSample(Sample) - Method in class net.sourceforge.seqware.common.model.WorkflowParam
-
Setter for the field sample.
- setSample(String) - Method in class net.sourceforge.seqware.pipeline.plugins.filelinker.FileLinkerLine
-
- setSample(Sample) - Method in class net.sourceforge.solexatools.webapp.metamodel.StudySampleReportLineItem
-
Setter for the field sample.
- setSample_url(String) - Method in class net.sourceforge.seqware.webservice.dto.IusDto
-
Setter for the field sample_url.
- setSampleAttribute(String, String) - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.SampleInfo
-
Adds a new sample attribute if the tag does not exist for this sample, or
changes the value of an existing sample attribute.
- setSampleAttributeCollection(Collection<SampleAttribute>) - Method in class io.seqware.webservice.generated.model.Sample
-
- setSampleAttributeId(Integer) - Method in class io.seqware.webservice.generated.model.SampleAttribute
-
- setSampleAttributeId(int) - Method in class net.sourceforge.seqware.common.model.SampleAttribute
-
Setter for the field sampleAttributeId.
- setSampleAttributes(Set<SampleAttribute>) - Method in class net.sourceforge.seqware.common.model.Sample
-
Setter for the field
sampleAttributes.
- setSampleAttributes(Set<TagValueUnit>) - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.SampleInfo
-
Set the value of sampleAttributes
- setSampleCode(String) - Method in class net.sourceforge.seqware.common.model.Lane
-
Setter for the field sampleCode.
- setSampleCollection(Collection<Sample>) - Method in class io.seqware.webservice.generated.model.Experiment
-
- setSampleCollection(Collection<Sample>) - Method in class io.seqware.webservice.generated.model.Organism
-
- setSampleCollection(Collection<Sample>) - Method in class io.seqware.webservice.generated.model.Registration
-
- setSampleCollection(Collection<Sample>) - Method in class io.seqware.webservice.generated.model.Sample
-
- setSampleCollection1(Collection<Sample>) - Method in class io.seqware.webservice.generated.model.Sample
-
- setSampleDAO(SampleDAO) - Method in class net.sourceforge.seqware.common.business.impl.FileUploadServiceImpl
-
Setter for the field sampleDAO.
- setSampleDAO(SampleDAO) - Method in class net.sourceforge.seqware.common.business.impl.SampleServiceImpl
-
setSampleDAO.
- setSampleDAO(SampleDAO) - Method in interface net.sourceforge.seqware.common.business.SampleService
-
setSampleDAO.
- setSampleDescription(String) - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.SampleInfo
-
Set the value of sampleDescription
- setSampleForStudy(Sample, HttpServletRequest) - Static method in class net.sourceforge.solexatools.util.SetNodeIdInSession
-
setSampleForStudy.
- setSampleForWorkflowRun(Sample, HttpServletRequest) - Static method in class net.sourceforge.solexatools.util.SetNodeIdInSession
-
setSampleForWorkflowRun.
- setSampleForWorkflowRunRunning(Sample, HttpServletRequest) - Static method in class net.sourceforge.solexatools.util.SetNodeIdInSession
-
setSampleForWorkflowRunRunning.
- setSampleHierarchies(List<SampleHierarchy>) - Method in class net.sourceforge.seqware.queryengine.webservice.model.SampleHierarchies
-
- setSampleId(Integer) - Method in class io.seqware.webservice.generated.model.FileReport
-
- setSampleId(Sample) - Method in class io.seqware.webservice.generated.model.Ius
-
- setSampleId(Sample) - Method in class io.seqware.webservice.generated.model.Lane
-
- setSampleId(Sample) - Method in class io.seqware.webservice.generated.model.ProcessingSamples
-
- setSampleId(Integer) - Method in class io.seqware.webservice.generated.model.Sample
-
- setSampleId(Sample) - Method in class io.seqware.webservice.generated.model.SampleAttribute
-
- setSampleId(Sample) - Method in class io.seqware.webservice.generated.model.SampleLink
-
- setSampleId(Sample) - Method in class io.seqware.webservice.generated.model.SampleSearch
-
- setSampleId(SequencerRun) - Method in class io.seqware.webservice.generated.model.SequencerRunAttribute
-
- setSampleId(Sample) - Method in class io.seqware.webservice.generated.model.ShareSample
-
- setSampleId(Integer) - Method in class net.sourceforge.seqware.common.model.Sample
-
Setter for the field
sampleId.
- setSampleId(Integer) - Method in class net.sourceforge.seqware.common.model.UploadSequence
-
Setter for the field sampleId.
- setSampleId(int) - Method in class net.sourceforge.seqware.queryengine.webservice.model.SampleHierarchy
-
- setSampleId(String) - Method in class net.sourceforge.seqware.webservice.dto.LibraryIdentityDto
-
Setter for the field sampleId.
- setSampleLinkCollection(Collection<SampleLink>) - Method in class io.seqware.webservice.generated.model.Sample
-
- setSampleLinkId(Integer) - Method in class io.seqware.webservice.generated.model.SampleLink
-
- setSampleLinkId(int) - Method in class net.sourceforge.seqware.common.model.SampleLink
-
Setter for the field sampleLinkId.
- setSampleLinks(Set<SampleLink>) - Method in class net.sourceforge.seqware.common.model.Sample
-
Setter for the field
sampleLinks.
- setSampleRelationshipCollection(Collection<SampleRelationship>) - Method in class io.seqware.webservice.generated.model.Sample
-
- setSampleRelationshipCollection1(Collection<SampleRelationship>) - Method in class io.seqware.webservice.generated.model.Sample
-
- setSampleRelationshipId(Integer) - Method in class io.seqware.webservice.generated.model.SampleRelationship
-
- setSampleReportDAO(SampleReportDAO) - Method in class net.sourceforge.seqware.common.business.impl.SampleReportServiceImpl
-
Setter for the field sampleReportDAO.
- setSampleReportService(SampleReportService) - Method in class net.sourceforge.seqware.common.ContextImpl
-
Setter for the field sampleReportService.
- setSampleReportService(SampleReportService) - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunReportTableController
-
Setter for the field sampleReportService.
- setSampleReportService(SampleReportService) - Method in class net.sourceforge.solexatools.webapp.controller.StudyReportBoxController
-
Setter for the field sampleReportService.
- setSampleReportService(SampleReportService) - Method in class net.sourceforge.solexatools.webapp.controller.StudyReportTableController
-
Setter for the field sampleReportService.
- setSamples(SortedSet<Sample>) - Method in class net.sourceforge.seqware.common.model.Experiment
-
Setter for the field samples.
- setSamples(Set<Sample>) - Method in class net.sourceforge.seqware.common.model.Processing
-
Setter for the field samples.
- setSamples(SortedSet<Sample>) - Method in class net.sourceforge.seqware.common.model.WorkflowRun
-
Setter for the field samples.
- setSamples(Set<SampleInfo>) - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.LaneInfo
-
Set the value of samples
- setSampleSearch(SampleSearch) - Method in class net.sourceforge.seqware.common.model.SampleSearchAttribute
-
Setter for the field sampleSearch.
- setSampleSearchAttributeCollection(Collection<SampleSearchAttribute>) - Method in class io.seqware.webservice.generated.model.SampleSearch
-
- setSampleSearchAttributeId(Integer) - Method in class io.seqware.webservice.generated.model.SampleSearchAttribute
-
- setSampleSearchAttributeId(Integer) - Method in class net.sourceforge.seqware.common.model.SampleSearchAttribute
-
Setter for the field sampleSearchAttributeId.
- setSampleSearchAttributes(Set<SampleSearchAttribute>) - Method in class net.sourceforge.seqware.common.model.SampleSearch
-
Setter for the field sampleSearchAttributes.
- setSampleSearchCollection(Collection<SampleSearch>) - Method in class io.seqware.webservice.generated.model.Sample
-
- setSampleSearchId(Integer) - Method in class io.seqware.webservice.generated.model.SampleSearch
-
- setSampleSearchId(SampleSearch) - Method in class io.seqware.webservice.generated.model.SampleSearchAttribute
-
- setSampleSearchId(Integer) - Method in class net.sourceforge.seqware.common.model.SampleSearch
-
Setter for the field sampleSearchId.
- setSampleService(SampleService) - Method in class net.sourceforge.seqware.common.ContextImpl
-
Setter for the field sampleService.
- setSampleService(SampleService) - Method in class net.sourceforge.solexatools.validation.SampleValidator
-
Setter for the field sampleService.
- setSampleService(SampleService) - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysBulkDownloadListDetailsController
-
Setter for the field sampleService.
- setSampleService(SampleService) - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysListDetailsController
-
Setter for the field sampleService.
- setSampleService(SampleService) - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysRunningListDetailsController
-
Setter for the field sampleService.
- setSampleService(SampleService) - Method in class net.sourceforge.solexatools.webapp.controller.BulkDownloadListDetailsController
-
Setter for the field sampleService.
- setSampleService(SampleService) - Method in class net.sourceforge.solexatools.webapp.controller.DownloadFileListController
-
Setter for the field sampleService.
- setSampleService(SampleService) - Method in class net.sourceforge.solexatools.webapp.controller.EntityController
-
Setter for the field sampleService.
- setSampleService(SampleService) - Method in class net.sourceforge.solexatools.webapp.controller.LaneController
-
Setter for the field sampleService.
- setSampleService(SampleService) - Method in class net.sourceforge.solexatools.webapp.controller.LaneSampleAssociateController
-
Setter for the field sampleService.
- setSampleService(SampleService) - Method in class net.sourceforge.solexatools.webapp.controller.LaneSampleAssociateSetupController
-
Setter for the field sampleService.
- setSampleService(SampleService) - Method in class net.sourceforge.solexatools.webapp.controller.LaunchWorkflowListDetailsController
-
Setter for the field sampleService.
- setSampleService(SampleService) - Method in class net.sourceforge.solexatools.webapp.controller.SampleController
-
Setter for the field sampleService.
- setSampleService(SampleService) - Method in class net.sourceforge.solexatools.webapp.controller.SampleSetupController
-
Setter for the field sampleService.
- setSampleService(SampleService) - Method in class net.sourceforge.solexatools.webapp.controller.SampleWorkflowRunsController
-
Setter for the field sampleService.
- setSampleService(SampleService) - Method in class net.sourceforge.solexatools.webapp.controller.SaveOpenNodeController
-
Setter for the field sampleService.
- setSampleService(SampleService) - Method in class net.sourceforge.solexatools.webapp.controller.SearchResultsListController
-
Setter for the field sampleService.
- setSampleService(SampleService) - Method in class net.sourceforge.solexatools.webapp.controller.SelectInputListController
-
Setter for the field sampleService.
- setSampleService(SampleService) - Method in class net.sourceforge.solexatools.webapp.controller.StudyListDetailsController
-
Setter for the field sampleService.
- setSampleService(SampleService) - Method in class net.sourceforge.solexatools.webapp.controller.StudyListDetailsFlatController
-
Setter for the field sampleService.
- setSampleService(SampleService) - Method in class net.sourceforge.solexatools.webapp.controller.StudyReportBoxController
-
Setter for the field sampleService.
- setSampleService(SampleService) - Method in class net.sourceforge.solexatools.webapp.controller.StudyReportTableController
-
Setter for the field sampleService.
- setSampleService(SampleService) - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileController
-
Setter for the field sampleService.
- setSampleService(SampleService) - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileSetupController
-
Setter for the field sampleService.
- setSampleService(SampleService) - Method in class net.sourceforge.solexatools.webapp.controller.UploadSequenceController
-
Setter for the field sampleService.
- setSampleService(SampleService) - Method in class net.sourceforge.solexatools.webapp.controller.UploadSequenceSetupController
-
Setter for the field sampleService.
- setSampleSwas(Set<String>) - Method in class net.sourceforge.seqware.common.business.impl.ValidationReportServiceImpl.ReportEntry
-
- setSampleType(String) - Method in class net.sourceforge.seqware.common.model.Lane
-
Setter for the field sampleType.
- setSampleUrl(String) - Method in class net.sourceforge.seqware.webservice.dto.SampleSearchDto
-
Setter for the field sampleUrl.
- setScientificName(String) - Method in class io.seqware.webservice.generated.model.Sample
-
- setSelection(LibrarySelection) - Method in class io.seqware.webservice.generated.model.ExperimentLibraryDesign
-
- setSelection(LibrarySelection) - Method in class net.sourceforge.seqware.common.model.ExperimentLibraryDesign
-
Setter for the field selection.
- setSender(MailSender) - Method in class net.sourceforge.solexatools.webapp.controller.InviteNewUserController
-
Setter for the field sender.
- setSequencer_run_url(String) - Method in class net.sourceforge.seqware.webservice.dto.IusDto
-
Setter for the field sequencer_run_url.
- setSequencerRun(SequencerRun) - Method in class net.sourceforge.seqware.common.model.Lane
-
Setter for the field sequencerRun.
- setSequencerRun(SequencerRun) - Method in class net.sourceforge.seqware.common.model.ProcessingSequencerRuns
-
Setter for the field sequencerRun.
- setSequencerRun(SequencerRun) - Method in class net.sourceforge.seqware.common.model.SampleReportRow
-
Setter for the field sequencerRun.
- setSequencerRun(SequencerRun) - Method in class net.sourceforge.seqware.common.model.SequencerRunReportId
-
Setter for the field sequencerRun.
- setSequencerRun(String) - Method in class net.sourceforge.seqware.pipeline.plugins.filelinker.FileLinkerLine
-
- setSequencerRun(Integer, HttpServletRequest) - Static method in class net.sourceforge.solexatools.util.SetNodeIdInSession
-
setSequencerRun.
- setSequencerRunAttributeCollection(Collection<SequencerRunAttribute>) - Method in class io.seqware.webservice.generated.model.SequencerRun
-
- setSequencerRunAttributeId(Integer) - Method in class io.seqware.webservice.generated.model.SequencerRunAttribute
-
- setSequencerRunAttributeId(Integer) - Method in class net.sourceforge.seqware.common.model.SequencerRunAttribute
-
Setter for the field sequencerRunAttributeId.
- setSequencerRunAttributes(Set<SequencerRunAttribute>) - Method in class net.sourceforge.seqware.common.model.SequencerRun
-
Setter for the field sequencerRunAttributes.
- setSequencerRunCollection(Collection<SequencerRun>) - Method in class io.seqware.webservice.generated.model.Platform
-
- setSequencerRunCollection(Collection<SequencerRun>) - Method in class io.seqware.webservice.generated.model.Registration
-
- setSequencerRunDAO(SequencerRunDAO) - Method in class net.sourceforge.seqware.common.business.impl.FileUploadServiceImpl
-
Setter for the field sequencerRunDAO.
- setSequencerRunDAO(SequencerRunDAO) - Method in class net.sourceforge.seqware.common.business.impl.SequencerRunServiceImpl
-
setSequencerRunDAO.
- setSequencerRunDAO(SequencerRunDAO) - Method in interface net.sourceforge.seqware.common.business.SequencerRunService
-
setSequencerRunDAO.
- setSequencerRunId(SequencerRun) - Method in class io.seqware.webservice.generated.model.Lane
-
- setSequencerRunId(SequencerRun) - Method in class io.seqware.webservice.generated.model.ProcessingSequencerRuns
-
- setSequencerRunId(Integer) - Method in class io.seqware.webservice.generated.model.SampleReport
-
- setSequencerRunId(Integer) - Method in class io.seqware.webservice.generated.model.SequencerRun
-
- setSequencerRunId(Integer) - Method in class net.sourceforge.seqware.common.model.SequencerRun
-
Setter for the field sequencerRunId.
- setSequencerRunId(Integer) - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
-
Setter for the field sequencerRunId.
- setSequencerRuns(Set<SequencerRun>) - Method in class net.sourceforge.seqware.common.model.Processing
-
Setter for the field sequencerRuns.
- setSequencerRunService(SequencerRunService) - Method in class net.sourceforge.seqware.common.ContextImpl
-
Setter for the field sequencerRunService.
- setSequencerRunService(SequencerRunService) - Method in class net.sourceforge.solexatools.validation.SequencerRunValidator
-
Setter for the field sequencerRunService.
- setSequencerRunService(SequencerRunService) - Method in class net.sourceforge.solexatools.webapp.controller.EntityController
-
Setter for the field sequencerRunService.
- setSequencerRunService(SequencerRunService) - Method in class net.sourceforge.solexatools.webapp.controller.ProcessingController
-
Setter for the field sequencerRunService.
- setSequencerRunService(SequencerRunService) - Method in class net.sourceforge.solexatools.webapp.controller.ProcessingSetupController
-
Setter for the field sequencerRunService.
- setSequencerRunService(SequencerRunService) - Method in class net.sourceforge.solexatools.webapp.controller.SearchResultsListController
-
Setter for the field sequencerRunService.
- setSequencerRunService(SequencerRunService) - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunController
-
Setter for the field sequencerRunService.
- setSequencerRunService(SequencerRunService) - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunControllerDTO
-
Setter for the field sequencerRunService.
- setSequencerRunService(SequencerRunService) - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunListController
-
Setter for the field sequencerRunService.
- setSequencerRunService(SequencerRunService) - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunListDetailsController
-
Setter for the field sequencerRunService.
- setSequencerRunService(SequencerRunService) - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunReportSetupController
-
Setter for the field sequencerRunService.
- setSequencerRunService(SequencerRunService) - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunReportTableController
-
Setter for the field sequencerRunService.
- setSequencerRunService(SequencerRunService) - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunSetupController
-
Setter for the field sequencerRunService.
- setSequencerRunService(SequencerRunService) - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunSetupControllerDTO
-
Setter for the field sequencerRunService.
- setSequencerRunService(SequencerRunService) - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunWizardController
-
Setter for the field sequencerRunService.
- setSequencerRunService(SequencerRunService) - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunWizardSetupController
-
Setter for the field sequencerRunService.
- setSequencerRunService(SequencerRunService) - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileController
-
Setter for the field sequencerRunService.
- setSequencerRunService(SequencerRunService) - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileSetupController
-
Setter for the field sequencerRunService.
- setSequencerRunService(SequencerRunService) - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowRunController
-
Setter for the field sequencerRunService.
- setSequencerRunSwas(Set<String>) - Method in class net.sourceforge.seqware.common.business.impl.ValidationReportServiceImpl.ReportEntry
-
- setSequencerRunValidator(Validator) - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunWizardController
-
Setter for the field sequencerRunValidator.
- setSequencerRunWizardDTO(SequencerRunWizardDTO) - Method in class net.sourceforge.seqware.common.model.SequencerRunAttribute
-
setSequencerRunWizardDTO.
- setSequencerRunWizardValidator(Validator) - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunWizardController
-
Setter for the field sequencerRunWizardValidator.
- setSequenceSpace(String) - Method in class io.seqware.webservice.generated.model.Experiment
-
- setSequenceSpace(String) - Method in class net.sourceforge.seqware.common.model.Experiment
-
Setter for the field sequenceSpace.
- setSeqwareAccession(Integer) - Method in class net.sourceforge.seqware.pipeline.plugins.filelinker.FileLinkerLine
-
- setSeqwareAccessionString(String) - Method in class net.sourceforge.seqware.pipeline.plugins.filelinker.FileLinkerLine
-
- setSeqwareRevision(String) - Method in class io.seqware.webservice.generated.model.WorkflowRun
-
- setSeqwareRevision(String) - Method in class net.sourceforge.seqware.common.model.WorkflowRun
-
Setter for the field seqwareRevision.
- setSeqwareVersion(String) - Method in class io.seqware.webservice.generated.model.Workflow
-
- setSeqwareVersion(String) - Method in class net.sourceforge.seqware.common.model.Workflow
-
Setter for the field seqwareVersion.
- setSessionFactory(SessionFactory) - Method in class net.sourceforge.seqware.common.ContextImpl
-
Setter for the field sessionFactory.
- setSharedStudies(SortedSet<ShareStudy>) - Method in class net.sourceforge.seqware.common.model.Study
-
Setter for the field sharedStudies.
- setSharedWorkflowRuns(SortedSet<ShareWorkflowRun>) - Method in class net.sourceforge.seqware.common.model.WorkflowRun
-
Setter for the field sharedWorkflowRuns.
- setShareExperimentCollection(Collection<ShareExperiment>) - Method in class io.seqware.webservice.generated.model.Experiment
-
- setShareExperimentCollection(Collection<ShareExperiment>) - Method in class io.seqware.webservice.generated.model.Registration
-
- setShareExperimentDAO(ShareExperimentDAO) - Method in class net.sourceforge.seqware.common.business.impl.ShareExperimentServiceImpl
-
setShareExperimentDAO.
- setShareExperimentDAO(ShareExperimentDAO) - Method in interface net.sourceforge.seqware.common.business.ShareExperimentService
-
setShareExperimentDAO.
- setShareExperimentId(Integer) - Method in class io.seqware.webservice.generated.model.ShareExperiment
-
- setShareExperimentId(int) - Method in class net.sourceforge.seqware.common.model.ShareExperiment
-
Setter for the field shareExperimentId.
- setShareFileCollection(Collection<ShareFile>) - Method in class io.seqware.webservice.generated.model.File
-
- setShareFileCollection(Collection<ShareFile>) - Method in class io.seqware.webservice.generated.model.Registration
-
- setShareFileDAO(ShareFileDAO) - Method in class net.sourceforge.seqware.common.business.impl.ShareFileServiceImpl
-
setShareFileDAO.
- setShareFileDAO(ShareFileDAO) - Method in interface net.sourceforge.seqware.common.business.ShareFileService
-
setShareFileDAO.
- setShareFileId(Integer) - Method in class io.seqware.webservice.generated.model.ShareFile
-
- setShareFileId(int) - Method in class net.sourceforge.seqware.common.model.ShareFile
-
Setter for the field shareFileId.
- setShareLaneCollection(Collection<ShareLane>) - Method in class io.seqware.webservice.generated.model.Lane
-
- setShareLaneCollection(Collection<ShareLane>) - Method in class io.seqware.webservice.generated.model.Registration
-
- setShareLaneDAO(ShareLaneDAO) - Method in class net.sourceforge.seqware.common.business.impl.ShareLaneServiceImpl
-
setShareLaneDAO.
- setShareLaneDAO(ShareLaneDAO) - Method in interface net.sourceforge.seqware.common.business.ShareLaneService
-
setShareLaneDAO.
- setShareLaneId(Integer) - Method in class io.seqware.webservice.generated.model.ShareLane
-
- setShareLaneId(int) - Method in class net.sourceforge.seqware.common.model.ShareLane
-
Setter for the field shareLaneId.
- setShareProcessingCollection(Collection<ShareProcessing>) - Method in class io.seqware.webservice.generated.model.Processing
-
- setShareProcessingCollection(Collection<ShareProcessing>) - Method in class io.seqware.webservice.generated.model.Registration
-
- setShareProcessingDAO(ShareProcessingDAO) - Method in class net.sourceforge.seqware.common.business.impl.ShareProcessingServiceImpl
-
setShareProcessingDAO.
- setShareProcessingDAO(ShareProcessingDAO) - Method in interface net.sourceforge.seqware.common.business.ShareProcessingService
-
setShareProcessingDAO.
- setShareProcessingId(Integer) - Method in class io.seqware.webservice.generated.model.ShareProcessing
-
- setShareProcessingId(int) - Method in class net.sourceforge.seqware.common.model.ShareProcessing
-
Setter for the field shareProcessingId.
- setShareSampleCollection(Collection<ShareSample>) - Method in class io.seqware.webservice.generated.model.Registration
-
- setShareSampleCollection(Collection<ShareSample>) - Method in class io.seqware.webservice.generated.model.Sample
-
- setShareSampleDAO(ShareSampleDAO) - Method in class net.sourceforge.seqware.common.business.impl.ShareSampleServiceImpl
-
setShareSampleDAO.
- setShareSampleDAO(ShareSampleDAO) - Method in interface net.sourceforge.seqware.common.business.ShareSampleService
-
setShareSampleDAO.
- setShareSampleId(Integer) - Method in class io.seqware.webservice.generated.model.ShareSample
-
- setShareSampleId(int) - Method in class net.sourceforge.seqware.common.model.ShareSample
-
Setter for the field shareSampleId.
- setShareStudyCollection(Collection<ShareStudy>) - Method in class io.seqware.webservice.generated.model.Registration
-
- setShareStudyCollection(Collection<ShareStudy>) - Method in class io.seqware.webservice.generated.model.Study
-
- setShareStudyDAO(ShareStudyDAO) - Method in class net.sourceforge.seqware.common.business.impl.ShareStudyServiceImpl
-
setShareStudyDAO.
- setShareStudyDAO(ShareStudyDAO) - Method in interface net.sourceforge.seqware.common.business.ShareStudyService
-
setShareStudyDAO.
- setShareStudyId(Integer) - Method in class io.seqware.webservice.generated.model.ShareStudy
-
- setShareStudyId(Integer) - Method in class net.sourceforge.seqware.common.model.ShareStudy
-
Setter for the field shareStudyId.
- setShareStudyService(ShareStudyService) - Method in class net.sourceforge.solexatools.webapp.controller.ShareValidatorController
-
Setter for the field shareStudyService.
- setShareStudyService(ShareStudyService) - Method in class net.sourceforge.solexatools.webapp.controller.StudyController
-
Setter for the field shareStudyService.
- setShareWorkflowRunCollection(Collection<ShareWorkflowRun>) - Method in class io.seqware.webservice.generated.model.Registration
-
- setShareWorkflowRunCollection(Collection<ShareWorkflowRun>) - Method in class io.seqware.webservice.generated.model.WorkflowRun
-
- setShareWorkflowRunDAO(ShareWorkflowRunDAO) - Method in class net.sourceforge.seqware.common.business.impl.ShareWorkflowRunServiceImpl
-
setShareWorkflowRunDAO.
- setShareWorkflowRunDAO(ShareWorkflowRunDAO) - Method in interface net.sourceforge.seqware.common.business.ShareWorkflowRunService
-
setShareWorkflowRunDAO.
- setShareWorkflowRunId(Integer) - Method in class io.seqware.webservice.generated.model.ShareWorkflowRun
-
- setShareWorkflowRunId(Integer) - Method in class net.sourceforge.seqware.common.model.ShareWorkflowRun
-
Setter for the field shareWorkflowRunId.
- setShareWorkflowRunService(ShareWorkflowRunService) - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysEventController
-
Setter for the field shareWorkflowRunService.
- setShareWorkflowRunService(ShareWorkflowRunService) - Method in class net.sourceforge.solexatools.webapp.controller.ShareValidatorController
-
Setter for the field shareWorkflowRunService.
- setSite(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object.Pfn
-
Setter for the field site.
- setSize(BigInteger) - Method in class io.seqware.webservice.generated.model.File
-
- setSize(Long) - Method in class net.sourceforge.seqware.common.model.File
-
Setter for the field size.
- setSize(Long) - Method in class net.sourceforge.seqware.common.module.FileMetadata
-
- setSize(Long) - Method in class net.sourceforge.seqware.pipeline.plugins.filelinker.FileLinkerLine
-
- setSize(Long) - Method in class net.sourceforge.seqware.webservice.dto.FileDto
-
Setter for the field size.
- setSizeString(String) - Method in class net.sourceforge.seqware.pipeline.plugins.filelinker.FileLinkerLine
-
- setSkip(Boolean) - Method in class io.seqware.webservice.generated.model.File
-
- setSkip(Boolean) - Method in class io.seqware.webservice.generated.model.Ius
-
- setSkip(Boolean) - Method in class io.seqware.webservice.generated.model.Lane
-
- setSkip(Boolean) - Method in class io.seqware.webservice.generated.model.Sample
-
- setSkip(Boolean) - Method in class io.seqware.webservice.generated.model.SequencerRun
-
- setSkip(Boolean) - Method in class net.sourceforge.seqware.common.model.File
-
- setSkip(Boolean) - Method in class net.sourceforge.seqware.common.model.IUS
-
Setter for the field skip.
- setSkip(Boolean) - Method in class net.sourceforge.seqware.common.model.Lane
-
Setter for the field skip.
- setSkip(Boolean) - Method in class net.sourceforge.seqware.common.model.Sample
-
Setter for the field
skip.
- setSkip(Boolean) - Method in class net.sourceforge.seqware.common.model.SequencerRun
-
Setter for the field skip.
- setSkip(Boolean) - Method in class net.sourceforge.seqware.webservice.dto.IusDto
-
Setter for the field skip.
- setSkipIfMissing(boolean) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.SqwFile
-
- setSlide1FilePath(String) - Method in class io.seqware.webservice.generated.model.SequencerRun
-
- setSlide1LaneCount(Integer) - Method in class io.seqware.webservice.generated.model.SequencerRun
-
- setSlide2FilePath(String) - Method in class io.seqware.webservice.generated.model.SequencerRun
-
- setSlide2LaneCount(Integer) - Method in class io.seqware.webservice.generated.model.SequencerRun
-
- setSlideCount(Integer) - Method in class io.seqware.webservice.generated.model.SequencerRun
-
- setSlideOneFilePath(String) - Method in class net.sourceforge.seqware.common.model.SequencerRun
-
Setter for the field slideOneFilePath.
- setSlideOneFilePath(String) - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
-
Setter for the field slideOneFilePath.
- setSlideOneLaneCount(Integer) - Method in class net.sourceforge.seqware.common.model.SequencerRun
-
Setter for the field slideOneLaneCount.
- setSlideOneLaneCount(Integer) - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
-
Setter for the field slideOneLaneCount.
- setSlideTwoFilePath(String) - Method in class net.sourceforge.seqware.common.model.SequencerRun
-
Setter for the field slideTwoFilePath.
- setSlideTwoFilePath(String) - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
-
Setter for the field slideTwoFilePath.
- setSlideTwoLaneCount(Integer) - Method in class net.sourceforge.seqware.common.model.SequencerRun
-
Setter for the field slideTwoLaneCount.
- setSlideTwoLaneCount(Integer) - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
-
Setter for the field slideTwoLaneCount.
- setSortable(boolean) - Method in class net.sourceforge.solexatools.webapp.metamodel.Flexigrid.ColumnModel
-
- setSortKeySample(Sample) - Method in class net.sourceforge.solexatools.webapp.metamodel.StudySampleReportLineItem
-
Setter for the field sortKeySample.
- setSource(LibrarySource) - Method in class io.seqware.webservice.generated.model.ExperimentLibraryDesign
-
- setSource(LibrarySource) - Method in class net.sourceforge.seqware.common.model.ExperimentLibraryDesign
-
Setter for the field source.
- setSourcePath(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.SqwFile
-
- setSpotDesignReadSpec(String) - Method in class net.sourceforge.seqware.common.model.Experiment
-
Setter for the field spotDesignReadSpec.
- setStartDate(Date) - Method in class io.seqware.webservice.generated.model.Invoice
-
- setStartDate(Date) - Method in class net.sourceforge.seqware.common.model.Invoice
-
Setter for the field startDate.
- setStartPage(String) - Method in class net.sourceforge.solexatools.util.PageInfo
-
Setter for the field startPage.
- setState(String) - Method in class io.seqware.webservice.generated.model.Invoice
-
- setState(InvoiceState) - Method in class net.sourceforge.seqware.common.model.Invoice
-
Setter for the field state.
- setStatus(String) - Method in class io.seqware.webservice.generated.model.Experiment
-
- setStatus(String) - Method in class io.seqware.webservice.generated.model.Processing
-
- setStatus(String) - Method in class io.seqware.webservice.generated.model.SampleReport
-
- setStatus(String) - Method in class io.seqware.webservice.generated.model.SequencerRun
-
- setStatus(String) - Method in class io.seqware.webservice.generated.model.Study
-
- setStatus(String) - Method in class io.seqware.webservice.generated.model.WorkflowRun
-
- setStatus(String) - Method in class net.sourceforge.seqware.common.model.Experiment
-
Setter for the field status.
- setStatus(ProcessingStatus) - Method in class net.sourceforge.seqware.common.model.Processing
-
- setStatus(String) - Method in class net.sourceforge.seqware.common.model.SampleReportRow
-
Setter for the field status.
- setStatus(SequencerRunStatus) - Method in class net.sourceforge.seqware.common.model.SequencerRun
-
Setter for the field status.
- setStatus(String) - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
-
Setter for the field status.
- setStatus(String) - Method in class net.sourceforge.seqware.common.model.Study
-
Setter for the field status.
- setStatus(WorkflowRunStatus) - Method in class net.sourceforge.seqware.common.model.WorkflowRun
-
Setter for the field status.
- setStatus(SequencerRunStatus) - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.RunInfo
-
Set the value of the sequencer run status
- setStatusCmd(String) - Method in class io.seqware.webservice.generated.model.WorkflowRun
-
- setStatusCmd(String) - Method in class net.sourceforge.seqware.common.model.WorkflowRun
-
Setter for the field statusCmd.
- setStatusCounts(int) - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowTools
-
Setter for the field statusCounts.
- setStatuses(String[]) - Method in class net.sourceforge.solexatools.webapp.metamodel.StudySampleReportLineItem
-
Setter for the field statuses.
- setStderr(String) - Method in class io.seqware.webservice.generated.model.Processing
-
- setStderr(String) - Method in class io.seqware.webservice.generated.model.WorkflowRun
-
- setStderr(String) - Method in class net.sourceforge.seqware.common.model.Processing
-
Setter for the field stderr.
- setStdErr(String) - Method in class net.sourceforge.seqware.common.model.WorkflowRun
-
Setter for the field stdErr.
- setStderr(String) - Method in class net.sourceforge.seqware.common.module.ReturnValue
-
Setter for the field stderr.
- setStderr(File) - Method in interface net.sourceforge.seqware.pipeline.module.RedirectAware
-
setStderr.
- setStderrFile(File) - Method in class net.sourceforge.seqware.pipeline.module.Module
-
Added by Xiaoshu Wang: Setter for the file that will be used to redirect
stderr
- setStdout(String) - Method in class io.seqware.webservice.generated.model.Processing
-
- setStdout(String) - Method in class io.seqware.webservice.generated.model.WorkflowRun
-
- setStdout(String) - Method in class net.sourceforge.seqware.common.model.Processing
-
Setter for the field stdout.
- setStdOut(String) - Method in class net.sourceforge.seqware.common.model.WorkflowRun
-
Setter for the field stdOut.
- setStdout(String) - Method in class net.sourceforge.seqware.common.module.ReturnValue
-
Setter for the field stdout.
- setStdout(File) - Method in interface net.sourceforge.seqware.pipeline.module.RedirectAware
-
setStdout.
- setStdoutFile(File) - Method in class net.sourceforge.seqware.pipeline.module.Module
-
Setter for the field stdoutFile.
- setStrategy(LibraryStrategy) - Method in class io.seqware.webservice.generated.model.ExperimentLibraryDesign
-
- setStrategy(LibraryStrategy) - Method in class net.sourceforge.seqware.common.model.ExperimentLibraryDesign
-
Setter for the field strategy.
- setStrExpectedNumberReads(String) - Method in class net.sourceforge.seqware.common.model.Experiment
-
Setter for the field strExpectedNumberReads.
- setStrExpectedNumberRuns(String) - Method in class net.sourceforge.seqware.common.model.Experiment
-
Setter for the field strExpectedNumberRuns.
- setStrExpectedNumReads(String) - Method in class net.sourceforge.seqware.common.model.Sample
-
Setter for the field
strExpectedNumReads.
- setStrExpectedNumRuns(String) - Method in class net.sourceforge.seqware.common.model.Sample
-
Setter for the field
strExpectedNumRuns.
- setStrLaneCount(String) - Method in class net.sourceforge.seqware.common.model.SequencerRunWizardDTO
-
Setter for the field strLaneCount.
- setStrRefLane(String) - Method in class net.sourceforge.seqware.common.model.SequencerRun
-
Setter for the field strRefLane.
- setStrStartURL(String) - Method in class net.sourceforge.seqware.common.business.UploadFile
-
Setter for the field strStartURL.
- setStrStartURL(String) - Method in class net.sourceforge.seqware.common.model.UploadSequence
-
Setter for the field strStartURL.
- setStudies(Set<Study>) - Method in class net.sourceforge.seqware.common.model.Processing
-
Setter for the field studies.
- setStudy(Study) - Method in class net.sourceforge.seqware.common.model.Experiment
-
Setter for the field study.
- setStudy(Study) - Method in class net.sourceforge.seqware.common.model.FileReportRow
-
Setter for the field study.
- setStudy(Study) - Method in class net.sourceforge.seqware.common.model.ProcessingStudies
-
Setter for the field study.
- setStudy(Study) - Method in class net.sourceforge.seqware.common.model.SampleReportRow
-
Setter for the field study.
- setStudy(Study) - Method in class net.sourceforge.seqware.common.model.SequencerRunReportId
-
Setter for the field study.
- setStudy(Study) - Method in class net.sourceforge.seqware.common.model.StudyAttribute
-
Setter for the field study.
- setStudy(Study) - Method in class net.sourceforge.seqware.common.model.StudyLink
-
Setter for the field study.
- setStudy(Integer, HttpServletRequest) - Static method in class net.sourceforge.solexatools.util.SetNodeIdInSession
-
setStudy.
- setStudyAttribute(String, String) - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.RunInfo
-
Adds a new study attribute if the tag does not exist for this study, or
changes the value of an existing study attribute.
- setStudyAttributeCollection(Collection<StudyAttribute>) - Method in class io.seqware.webservice.generated.model.Study
-
- setStudyAttributeId(Integer) - Method in class io.seqware.webservice.generated.model.StudyAttribute
-
- setStudyAttributeId(int) - Method in class net.sourceforge.seqware.common.model.StudyAttribute
-
Setter for the field studyAttributeId.
- setStudyAttributes(Set<StudyAttribute>) - Method in class net.sourceforge.seqware.common.model.Study
-
Setter for the field studyAttributes.
- setStudyAttributes(Set<TagValueUnit>) - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.RunInfo
-
Set the value of studyAttributes
- setStudyCenterName(String) - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.RunInfo
-
Set the value of studyCenterName
- setStudyCenterProject(String) - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.RunInfo
-
Set the value of studyCenterProject
- setStudyCollection(Collection<Study>) - Method in class io.seqware.webservice.generated.model.Registration
-
- setStudyCollection(Collection<Study>) - Method in class io.seqware.webservice.generated.model.StudyType
-
- setStudyDAO(StudyDAO) - Method in class net.sourceforge.seqware.common.business.impl.FileUploadServiceImpl
-
Setter for the field studyDAO.
- setStudyDAO(StudyDAO) - Method in class net.sourceforge.seqware.common.business.impl.StudyServiceImpl
-
setStudyDAO.
- setStudyDAO(StudyDAO) - Method in interface net.sourceforge.seqware.common.business.StudyService
-
setStudyDAO.
- setStudyDescription(String) - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.RunInfo
-
Set the value of studyDescription
- setStudyId(Study) - Method in class io.seqware.webservice.generated.model.Experiment
-
- setStudyId(Integer) - Method in class io.seqware.webservice.generated.model.FileReport
-
- setStudyId(Study) - Method in class io.seqware.webservice.generated.model.ProcessingStudies
-
- setStudyId(Integer) - Method in class io.seqware.webservice.generated.model.SampleReport
-
- setStudyId(Study) - Method in class io.seqware.webservice.generated.model.ShareStudy
-
- setStudyId(Integer) - Method in class io.seqware.webservice.generated.model.Study
-
- setStudyId(Study) - Method in class io.seqware.webservice.generated.model.StudyAttribute
-
- setStudyId(Study) - Method in class io.seqware.webservice.generated.model.StudyLink
-
- setStudyId(Integer) - Method in class net.sourceforge.seqware.common.model.ShareStudy
-
Setter for the field studyId.
- setStudyId(Integer) - Method in class net.sourceforge.seqware.common.model.Study
-
Setter for the field studyId.
- setStudyLinkCollection(Collection<StudyLink>) - Method in class io.seqware.webservice.generated.model.Study
-
- setStudyLinkId(Integer) - Method in class io.seqware.webservice.generated.model.StudyLink
-
- setStudyLinkId(int) - Method in class net.sourceforge.seqware.common.model.StudyLink
-
Setter for the field studyLinkId.
- setStudyLinks(Set<StudyLink>) - Method in class net.sourceforge.seqware.common.model.Study
-
Setter for the field studyLinks.
- setStudyService(StudyService) - Method in class net.sourceforge.seqware.common.ContextImpl
-
Setter for the field studyService.
- setStudyService(StudyService) - Method in class net.sourceforge.solexatools.validation.StudyValidator
-
Setter for the field studyService.
- setStudyService(StudyService) - Method in class net.sourceforge.solexatools.webapp.controller.BulkDownloadListController
-
Setter for the field studyService.
- setStudyService(StudyService) - Method in class net.sourceforge.solexatools.webapp.controller.BulkDownloadListDetailsController
-
Setter for the field studyService.
- setStudyService(StudyService) - Method in class net.sourceforge.solexatools.webapp.controller.DownloadFileListController
-
Setter for the field studyService.
- setStudyService(StudyService) - Method in class net.sourceforge.solexatools.webapp.controller.EntityController
-
Setter for the field studyService.
- setStudyService(StudyService) - Method in class net.sourceforge.solexatools.webapp.controller.ExperimentController
-
Setter for the field studyService.
- setStudyService(StudyService) - Method in class net.sourceforge.solexatools.webapp.controller.ExperimentSetupController
-
Setter for the field studyService.
- setStudyService(StudyService) - Method in class net.sourceforge.solexatools.webapp.controller.LaunchWorkflowListController
-
Setter for the field studyService.
- setStudyService(StudyService) - Method in class net.sourceforge.solexatools.webapp.controller.LaunchWorkflowListDetailsController
-
Setter for the field studyService.
- setStudyService(StudyService) - Method in class net.sourceforge.solexatools.webapp.controller.SearchResultsListController
-
Setter for the field studyService.
- setStudyService(StudyService) - Method in class net.sourceforge.solexatools.webapp.controller.SelectInputListController
-
Setter for the field studyService.
- setStudyService(StudyService) - Method in class net.sourceforge.solexatools.webapp.controller.ShareValidatorController
-
Setter for the field studyService.
- setStudyService(StudyService) - Method in class net.sourceforge.solexatools.webapp.controller.StudyController
-
Setter for the field studyService.
- setStudyService(StudyService) - Method in class net.sourceforge.solexatools.webapp.controller.StudyListController
-
Setter for the field studyService.
- setStudyService(StudyService) - Method in class net.sourceforge.solexatools.webapp.controller.StudyListDetailsController
-
Setter for the field studyService.
- setStudyService(StudyService) - Method in class net.sourceforge.solexatools.webapp.controller.StudyListDetailsFlatController
-
Setter for the field studyService.
- setStudyService(StudyService) - Method in class net.sourceforge.solexatools.webapp.controller.StudyReportBoxController
-
Setter for the field studyService.
- setStudyService(StudyService) - Method in class net.sourceforge.solexatools.webapp.controller.StudyReportController
-
Setter for the field studyService.
- setStudyService(StudyService) - Method in class net.sourceforge.solexatools.webapp.controller.StudyReportSetupController
-
Setter for the field studyService.
- setStudyService(StudyService) - Method in class net.sourceforge.solexatools.webapp.controller.StudyReportTableController
-
Setter for the field studyService.
- setStudyService(StudyService) - Method in class net.sourceforge.solexatools.webapp.controller.StudySetupController
-
Setter for the field studyService.
- setStudyService(StudyService) - Method in class net.sourceforge.solexatools.webapp.controller.StudyTableController
-
- setStudyService(StudyService) - Method in class net.sourceforge.solexatools.webapp.controller.StudyTableControllerDetails
-
Setter for the field
studyService.
- setStudyService(StudyService) - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileController
-
Setter for the field studyService.
- setStudyService(StudyService) - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileSetupController
-
Setter for the field studyService.
- setStudySwas(Set<String>) - Method in class net.sourceforge.seqware.common.business.impl.ValidationReportServiceImpl.ReportEntry
-
- setStudyTitle(String) - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.RunInfo
-
Set the value of studyTitle
- setStudyType(StudyType) - Method in class io.seqware.webservice.generated.model.Lane
-
- setStudyType(StudyType) - Method in class net.sourceforge.seqware.common.model.Lane
-
- setStudyType(int) - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.RunInfo
-
- setStudyTypeAcc(int) - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.LaneInfo
-
Set the value of studyTypeAcc
- setStudyTypeDAO(StudyTypeDAO) - Method in class net.sourceforge.seqware.common.business.impl.StudyServiceImpl
-
Setter for the field studyTypeDAO.
- setStudyTypeDAO(StudyTypeDAO) - Method in class net.sourceforge.seqware.common.business.impl.StudyTypeServiceImpl
-
setStudyTypeDAO.
- setStudyTypeDAO(StudyTypeDAO) - Method in interface net.sourceforge.seqware.common.business.StudyTypeService
-
setStudyTypeDAO.
- setStudyTypeId(Integer) - Method in class io.seqware.webservice.generated.model.StudyType
-
- setStudyTypeId(Integer) - Method in class net.sourceforge.seqware.common.model.StudyType
-
Setter for the field studyTypeId.
- setStudyTypeService(StudyTypeService) - Method in class net.sourceforge.seqware.common.ContextImpl
-
- setStudyTypeService(StudyTypeService) - Method in class net.sourceforge.solexatools.webapp.controller.StudyController
-
Setter for the field studyTypeService.
- setStudyTypeService(StudyTypeService) - Method in class net.sourceforge.solexatools.webapp.controller.StudySetupController
-
Setter for the field studyTypeService.
- setSummaryLines(List<SummaryLine>) - Method in class net.sourceforge.solexatools.util.SummaryData
-
Setter for the field summaryLines.
- setSwa(Integer) - Method in class net.sourceforge.seqware.webservice.dto.IusDto
-
Setter for the field swa.
- setSwAccession(Integer) - Method in class io.seqware.webservice.generated.model.Expense
-
- setSwAccession(Integer) - Method in class io.seqware.webservice.generated.model.Experiment
-
- setSwAccession(Integer) - Method in class io.seqware.webservice.generated.model.File
-
- setSwAccession(Integer) - Method in class io.seqware.webservice.generated.model.Invoice
-
- setSwAccession(Integer) - Method in class io.seqware.webservice.generated.model.Ius
-
- setSwAccession(Integer) - Method in class io.seqware.webservice.generated.model.Lane
-
- setSwAccession(Integer) - Method in class io.seqware.webservice.generated.model.Processing
-
- setSwAccession(Integer) - Method in class io.seqware.webservice.generated.model.ProcessingExperiments
-
- setSwAccession(Integer) - Method in class io.seqware.webservice.generated.model.ProcessingIus
-
- setSwAccession(Integer) - Method in class io.seqware.webservice.generated.model.ProcessingLanes
-
- setSwAccession(Integer) - Method in class io.seqware.webservice.generated.model.ProcessingSamples
-
- setSwAccession(Integer) - Method in class io.seqware.webservice.generated.model.ProcessingSequencerRuns
-
- setSwAccession(Integer) - Method in class io.seqware.webservice.generated.model.ProcessingStudies
-
- setSwAccession(Integer) - Method in class io.seqware.webservice.generated.model.Sample
-
- setSwAccession(Integer) - Method in class io.seqware.webservice.generated.model.SequencerRun
-
- setSwAccession(Integer) - Method in class io.seqware.webservice.generated.model.ShareExperiment
-
- setSwAccession(Integer) - Method in class io.seqware.webservice.generated.model.ShareFile
-
- setSwAccession(Integer) - Method in class io.seqware.webservice.generated.model.ShareLane
-
- setSwAccession(Integer) - Method in class io.seqware.webservice.generated.model.ShareProcessing
-
- setSwAccession(Integer) - Method in class io.seqware.webservice.generated.model.ShareSample
-
- setSwAccession(Integer) - Method in class io.seqware.webservice.generated.model.ShareStudy
-
- setSwAccession(Integer) - Method in class io.seqware.webservice.generated.model.ShareWorkflowRun
-
- setSwAccession(Integer) - Method in class io.seqware.webservice.generated.model.Study
-
- setSwAccession(Integer) - Method in class io.seqware.webservice.generated.model.Workflow
-
- setSwAccession(Integer) - Method in class io.seqware.webservice.generated.model.WorkflowRun
-
- setSwAccession(Integer) - Method in class net.sourceforge.seqware.common.model.Expense
-
Setter for the field
swAccession.
- setSwAccession(Integer) - Method in class net.sourceforge.seqware.common.model.Experiment
-
Setter for the field swAccession.
- setSwAccession(Integer) - Method in class net.sourceforge.seqware.common.model.File
-
Setter for the field swAccession.
- setSwAccession(Integer) - Method in class net.sourceforge.seqware.common.model.Invoice
-
Setter for the field swAccession.
- setSwAccession(Integer) - Method in class net.sourceforge.seqware.common.model.IUS
-
Setter for the field swAccession.
- setSwAccession(Integer) - Method in class net.sourceforge.seqware.common.model.Lane
-
Setter for the field swAccession.
- setSwAccession(Integer) - Method in class net.sourceforge.seqware.common.model.Processing
-
Setter for the field swAccession.
- setSwAccession(Integer) - Method in class net.sourceforge.seqware.common.model.ProcessingExperiments
-
Setter for the field swAccession.
- setSwAccession(Integer) - Method in class net.sourceforge.seqware.common.model.ProcessingIus
-
Setter for the field swAccession.
- setSwAccession(Integer) - Method in class net.sourceforge.seqware.common.model.ProcessingLanes
-
Setter for the field swAccession.
- setSwAccession(Integer) - Method in class net.sourceforge.seqware.common.model.ProcessingSamples
-
Setter for the field swAccession.
- setSwAccession(Integer) - Method in class net.sourceforge.seqware.common.model.ProcessingSequencerRuns
-
Setter for the field swAccession.
- setSwAccession(Integer) - Method in class net.sourceforge.seqware.common.model.ProcessingStudies
-
Setter for the field swAccession.
- setSwAccession(Integer) - Method in class net.sourceforge.seqware.common.model.Sample
-
Setter for the field
swAccession.
- setSwAccession(Integer) - Method in class net.sourceforge.seqware.common.model.SequencerRun
-
Setter for the field swAccession.
- setSwAccession(Integer) - Method in class net.sourceforge.seqware.common.model.ShareExperiment
-
Setter for the field swAccession.
- setSwAccession(Integer) - Method in class net.sourceforge.seqware.common.model.ShareFile
-
Setter for the field swAccession.
- setSwAccession(Integer) - Method in class net.sourceforge.seqware.common.model.ShareLane
-
Setter for the field swAccession.
- setSwAccession(Integer) - Method in class net.sourceforge.seqware.common.model.ShareProcessing
-
Setter for the field swAccession.
- setSwAccession(Integer) - Method in class net.sourceforge.seqware.common.model.ShareSample
-
Setter for the field swAccession.
- setSwAccession(Integer) - Method in class net.sourceforge.seqware.common.model.ShareStudy
-
Setter for the field swAccession.
- setSwAccession(Integer) - Method in class net.sourceforge.seqware.common.model.ShareWorkflowRun
-
Setter for the field swAccession.
- setSwAccession(Integer) - Method in class net.sourceforge.seqware.common.model.Study
-
Setter for the field swAccession.
- setSwAccession(Integer) - Method in class net.sourceforge.seqware.common.model.Workflow
-
Setter for the field swAccession.
- setSwAccession(Integer) - Method in class net.sourceforge.seqware.common.model.WorkflowRun
-
Setter for the field swAccession.
- setSwCluster(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Environment
-
- setTag(String) - Method in class io.seqware.webservice.generated.model.ExpenseAttribute
-
- setTag(String) - Method in class io.seqware.webservice.generated.model.ExperimentAttribute
-
- setTag(String) - Method in class io.seqware.webservice.generated.model.FileAttribute
-
- setTag(String) - Method in class io.seqware.webservice.generated.model.InvoiceAttribute
-
- setTag(String) - Method in class io.seqware.webservice.generated.model.Ius
-
- setTag(String) - Method in class io.seqware.webservice.generated.model.IusAttribute
-
- setTag(String) - Method in class io.seqware.webservice.generated.model.LaneAttribute
-
- setTag(String) - Method in class io.seqware.webservice.generated.model.ProcessingAttribute
-
- setTag(String) - Method in class io.seqware.webservice.generated.model.SampleAttribute
-
- setTag(String) - Method in class io.seqware.webservice.generated.model.SampleSearchAttribute
-
- setTag(String) - Method in class io.seqware.webservice.generated.model.SequencerRunAttribute
-
- setTag(String) - Method in class io.seqware.webservice.generated.model.StudyAttribute
-
- setTag(String) - Method in class io.seqware.webservice.generated.model.WorkflowAttribute
-
- setTag(String) - Method in class io.seqware.webservice.generated.model.WorkflowRunAttribute
-
- setTag(String) - Method in interface net.sourceforge.seqware.common.model.Attribute
-
setTag.
- setTag(String) - Method in class net.sourceforge.seqware.common.model.ExperimentAttribute
-
Setter for the field tag.
- setTag(String) - Method in class net.sourceforge.seqware.common.model.FileAttribute
-
setTag.
- setTag(String) - Method in class net.sourceforge.seqware.common.model.IUS
-
Setter for the field tag.
- setTag(String) - Method in class net.sourceforge.seqware.common.model.IUSAttribute
-
setTag.
- setTag(String) - Method in class net.sourceforge.seqware.common.model.LaneAttribute
-
Setter for the field tag.
- setTag(String) - Method in class net.sourceforge.seqware.common.model.ProcessingAttribute
-
setTag.
- setTag(String) - Method in class net.sourceforge.seqware.common.model.SampleAttribute
-
setTag.
- setTag(String) - Method in class net.sourceforge.seqware.common.model.SampleSearchAttribute
-
setTag.
- setTag(String) - Method in class net.sourceforge.seqware.common.model.SequencerRunAttribute
-
setTag.
- setTag(String) - Method in class net.sourceforge.seqware.common.model.StudyAttribute
-
setTag.
- setTag(String) - Method in class net.sourceforge.seqware.common.model.WorkflowAttribute
-
setTag.
- setTag(String) - Method in class net.sourceforge.seqware.common.model.WorkflowRunAttribute
-
setTag.
- setTag(String) - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.TagValueUnit
-
- setTags(String) - Method in class io.seqware.webservice.generated.model.Lane
-
- setTags(String) - Method in class io.seqware.webservice.generated.model.Sample
-
- setTags(String) - Method in class net.sourceforge.seqware.common.model.Lane
-
Setter for the field tags.
- setTags(String) - Method in class net.sourceforge.seqware.common.model.Sample
-
Setter for the field
tags.
- setTags(Map<String, String>) - Method in class net.sourceforge.seqware.pipeline.workflowV2.AbstractWorkflowDataModel
-
set the key-value properties from metadata.xml
- setTagSpec(String) - Method in class io.seqware.webservice.generated.model.ExperimentSpotDesign
-
- setTagSpec(String) - Method in class net.sourceforge.seqware.common.model.ExperimentSpotDesign
-
Setter for the field tagSpec.
- setTargetedResequencing(String) - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.SampleInfo
-
Set the value of targetedResequencing and sets the
'geo_targeted_resequencing' attribute.
- setTaskGroup(Boolean) - Method in class io.seqware.webservice.generated.model.Processing
-
- setTaskGroup(boolean) - Method in class net.sourceforge.seqware.common.model.Processing
-
Setter for the field taskGroup.
- setTaxonId(Integer) - Method in class io.seqware.webservice.generated.model.Sample
-
- setTemplate(String) - Method in class net.sourceforge.seqware.common.model.Workflow
-
Setter for the field template.
- setTemplate(String) - Method in class net.sourceforge.seqware.common.model.WorkflowRun
-
Setter for the field template.
- setTemplatePath(String) - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowInfo
-
Setter for the field templatePath.
- setTemplateType(String) - Method in class net.sourceforge.solexatools.webapp.metamodel.StudySampleReportFileLineItem
-
Setter for the field templateType.
- setTest(Boolean) - Method in class net.sourceforge.seqware.pipeline.deciders.BasicDecider
-
- setTestCmd(String) - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowInfo
-
Setter for the field testCmd.
- setThreads(int) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.AbstractJob
-
- setThreads(int) - Method in interface net.sourceforge.seqware.pipeline.workflowV2.model.Job
-
set the max thread number
- setThreads(int) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.JobBatch
-
- setTimeTaken(String) - Method in class net.sourceforge.seqware.common.hibernate.reports.WorkflowRunReportRow
-
Setter for the field timeTaken.
- SETTINGSFILENOTFOUND - Static variable in class net.sourceforge.seqware.common.module.ReturnValue
-
Constant SETTINGSFILENOTFOUND=13
- setTissSource(String) - Method in class net.sourceforge.solexatools.webapp.metamodel.StudySampleReportFileLineItem
-
Setter for the field tissSource.
- setTissueOrigin(String) - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.SampleInfo
-
Set the value of tissueOrigin and sets the 'geo_tissue_origin' attribute.
- setTissuePreparation(String) - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.SampleInfo
-
Set the value of tissuePreparation, and sets the 'geo_tissue_preparation'
attribute.
- setTissueType(String) - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.SampleInfo
-
Set the value of tissueType and sets the 'geo_tissue_type' attribute.
- setTitle(String) - Method in class io.seqware.webservice.generated.model.Experiment
-
- setTitle(String) - Method in class io.seqware.webservice.generated.model.Sample
-
- setTitle(String) - Method in class io.seqware.webservice.generated.model.Study
-
- setTitle(String) - Method in class net.sourceforge.seqware.common.model.Experiment
-
Setter for the field title.
- setTitle(String) - Method in class net.sourceforge.seqware.common.model.Sample
-
Setter for the field
title.
- setTitle(String) - Method in class net.sourceforge.seqware.common.model.Study
-
Setter for the field title.
- setTotal(int) - Method in class net.sourceforge.solexatools.webapp.metamodel.Flexigrid
-
Setter for the field total.
- setTotalPrice(BigInteger) - Method in class io.seqware.webservice.generated.model.Expense
-
- setTotalPrice(Double) - Method in class net.sourceforge.seqware.common.model.Expense
-
Setter for the field
totalPrice.
- setTotalUnits(BigInteger) - Method in class io.seqware.webservice.generated.model.Expense
-
- setTotalUnits(Double) - Method in class net.sourceforge.seqware.common.model.Expense
-
Setter for the field
totalUnits.
- setType(String) - Method in class io.seqware.webservice.generated.model.File
-
- setType(LaneType) - Method in class io.seqware.webservice.generated.model.Lane
-
- setType(String) - Method in class io.seqware.webservice.generated.model.Sample
-
- setType(String) - Method in class io.seqware.webservice.generated.model.WorkflowParam
-
- setType(String) - Method in class io.seqware.webservice.generated.model.WorkflowRunParam
-
- setType(String) - Method in class net.sourceforge.seqware.common.model.File
-
Setter for the field type.
- setType(String) - Method in class net.sourceforge.seqware.common.model.Sample
-
Setter for the field
type.
- setType(String) - Method in class net.sourceforge.seqware.common.model.UploadSequence
-
Setter for the field type.
- setType(String) - Method in class net.sourceforge.seqware.common.model.WorkflowParam
-
Setter for the field type.
- setType(String) - Method in class net.sourceforge.seqware.common.model.WorkflowRunParam
-
Setter for the field type.
- setType(String) - Method in class net.sourceforge.seqware.common.module.FileMetadata
-
- setType(Requirement.Type) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Requirement
-
- setType(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.SqwFile
-
- setType(String) - Method in class net.sourceforge.seqware.webservice.dto.FileDto
-
Setter for the field type.
- setType(String) - Method in class net.sourceforge.solexatools.webapp.controller.SearchController
-
Setter for the field type.
- setTypeNode(String) - Method in class net.sourceforge.seqware.common.business.UploadFile
-
Setter for the field typeNode.
- setUnit(String) - Method in class io.seqware.webservice.generated.model.FileAttribute
-
- setUnit(String) - Method in class io.seqware.webservice.generated.model.WorkflowAttribute
-
- setUnit(String) - Method in class io.seqware.webservice.generated.model.WorkflowRunAttribute
-
- setUnit(String) - Method in interface net.sourceforge.seqware.common.model.Attribute
-
setUnit.
- setUnit(String) - Method in class net.sourceforge.seqware.common.model.ExperimentAttribute
-
- setUnit(String) - Method in class net.sourceforge.seqware.common.model.FileAttribute
-
setUnit.
- setUnit(String) - Method in class net.sourceforge.seqware.common.model.IUSAttribute
-
setUnit.
- setUnit(String) - Method in class net.sourceforge.seqware.common.model.LaneAttribute
-
- setUnit(String) - Method in class net.sourceforge.seqware.common.model.ProcessingAttribute
-
setUnit.
- setUnit(String) - Method in class net.sourceforge.seqware.common.model.SampleAttribute
-
setUnit.
- setUnit(String) - Method in class net.sourceforge.seqware.common.model.SampleSearchAttribute
-
setUnit.
- setUnit(String) - Method in class net.sourceforge.seqware.common.model.SequencerRunAttribute
-
setUnit.
- setUnit(String) - Method in class net.sourceforge.seqware.common.model.StudyAttribute
-
setUnit.
- setUnit(String) - Method in class net.sourceforge.seqware.common.model.WorkflowAttribute
-
setUnit.
- setUnit(String) - Method in class net.sourceforge.seqware.common.model.WorkflowRunAttribute
-
setUnit.
- setUnit(String) - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.TagValueUnit
-
- setUnit(String) - Method in class net.sourceforge.seqware.webservice.dto.AttributeDto
-
Setter for the field unit.
- setUnits(String) - Method in class io.seqware.webservice.generated.model.ExpenseAttribute
-
- setUnits(String) - Method in class io.seqware.webservice.generated.model.ExperimentAttribute
-
- setUnits(String) - Method in class io.seqware.webservice.generated.model.InvoiceAttribute
-
- setUnits(String) - Method in class io.seqware.webservice.generated.model.IusAttribute
-
- setUnits(String) - Method in class io.seqware.webservice.generated.model.LaneAttribute
-
- setUnits(String) - Method in class io.seqware.webservice.generated.model.ProcessingAttribute
-
- setUnits(String) - Method in class io.seqware.webservice.generated.model.SampleAttribute
-
- setUnits(String) - Method in class io.seqware.webservice.generated.model.SequencerRunAttribute
-
- setUnits(String) - Method in class io.seqware.webservice.generated.model.StudyAttribute
-
- setUnits(String) - Method in class net.sourceforge.seqware.common.model.ExperimentAttribute
-
Setter for the field units.
- setUnits(String) - Method in class net.sourceforge.seqware.common.model.IUSAttribute
-
Setter for the field units.
- setUnits(String) - Method in class net.sourceforge.seqware.common.model.LaneAttribute
-
Setter for the field units.
- setUnits(String) - Method in class net.sourceforge.seqware.common.model.ProcessingAttribute
-
Setter for the field units.
- setUnits(String) - Method in class net.sourceforge.seqware.common.model.SampleAttribute
-
Setter for the field units.
- setUnits(String) - Method in class net.sourceforge.seqware.common.model.SequencerRunAttribute
-
Setter for the field units.
- setUnits(String) - Method in class net.sourceforge.seqware.common.model.StudyAttribute
-
Setter for the field units.
- setup(String) - Static method in class net.sourceforge.seqware.common.util.freemarker.Freemarker
-
setup.
- setUpdateTimestamp(Date) - Method in class net.sourceforge.seqware.common.model.Experiment
-
Setter for the field updateTimestamp.
- setUpdateTimestamp(Date) - Method in class net.sourceforge.seqware.common.model.IUS
-
Setter for the field updateTimestamp.
- setUpdateTimestamp(Date) - Method in class net.sourceforge.seqware.common.model.Lane
-
Setter for the field updateTimestamp.
- setUpdateTimestamp(Date) - Method in class net.sourceforge.seqware.common.model.Processing
-
Setter for the field updateTimestamp.
- setUpdateTimestamp(Date) - Method in class net.sourceforge.seqware.common.model.Registration
-
Setter for the field updateTimestamp.
- setUpdateTimestamp(Date) - Method in class net.sourceforge.seqware.common.model.Sample
-
Setter for the field
updateTimestamp.
- setUpdateTimestamp(Date) - Method in class net.sourceforge.seqware.common.model.SequencerRun
-
Setter for the field updateTimestamp.
- setUpdateTimestamp(Date) - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
-
Setter for the field updateTimestamp.
- setUpdateTimestamp(Date) - Method in class net.sourceforge.seqware.common.model.ShareStudy
-
Setter for the field updateTimestamp.
- setUpdateTimestamp(Date) - Method in class net.sourceforge.seqware.common.model.ShareWorkflowRun
-
Setter for the field updateTimestamp.
- setUpdateTimestamp(Date) - Method in class net.sourceforge.seqware.common.model.Study
-
Setter for the field updateTimestamp.
- setUpdateTimestamp(Date) - Method in class net.sourceforge.seqware.common.model.Workflow
-
Setter for the field updateTimestamp.
- setUpdateTimestamp(Date) - Method in class net.sourceforge.seqware.common.model.WorkflowRun
-
Setter for the field updateTimestamp.
- setUpdateTimeStamp(String) - Method in class net.sourceforge.seqware.webservice.dto.IusDto
-
Setter for the field updateTimeStamp.
- setUpdateTimeStamp(String) - Method in class net.sourceforge.seqware.webservice.dto.LibraryDto
-
Setter for the field updateTimeStamp.
- setUpdateTstmp(Timestamp) - Method in class io.seqware.webservice.generated.model.Experiment
-
- setUpdateTstmp(Timestamp) - Method in class io.seqware.webservice.generated.model.Ius
-
- setUpdateTstmp(Timestamp) - Method in class io.seqware.webservice.generated.model.Lane
-
- setUpdateTstmp(Timestamp) - Method in class io.seqware.webservice.generated.model.Processing
-
- setUpdateTstmp(Timestamp) - Method in class io.seqware.webservice.generated.model.Sample
-
- setUpdateTstmp(Timestamp) - Method in class io.seqware.webservice.generated.model.SequencerRun
-
- setUpdateTstmp(Date) - Method in class io.seqware.webservice.generated.model.ShareExperiment
-
- setUpdateTstmp(Date) - Method in class io.seqware.webservice.generated.model.ShareFile
-
- setUpdateTstmp(Date) - Method in class io.seqware.webservice.generated.model.ShareLane
-
- setUpdateTstmp(Date) - Method in class io.seqware.webservice.generated.model.ShareProcessing
-
- setUpdateTstmp(Date) - Method in class io.seqware.webservice.generated.model.ShareSample
-
- setUpdateTstmp(Date) - Method in class io.seqware.webservice.generated.model.ShareStudy
-
- setUpdateTstmp(Date) - Method in class io.seqware.webservice.generated.model.ShareWorkflowRun
-
- setUpdateTstmp(Timestamp) - Method in class io.seqware.webservice.generated.model.Study
-
- setUpdateTstmp(Timestamp) - Method in class io.seqware.webservice.generated.model.Workflow
-
- setUpdateTstmp(Timestamp) - Method in class io.seqware.webservice.generated.model.WorkflowRun
-
- setUpdateTstmp(Date) - Method in class net.sourceforge.seqware.common.model.ShareExperiment
-
Setter for the field updateTstmp.
- setUpdateTstmp(Date) - Method in class net.sourceforge.seqware.common.model.ShareFile
-
Setter for the field updateTstmp.
- setUpdateTstmp(Date) - Method in class net.sourceforge.seqware.common.model.ShareLane
-
Setter for the field updateTstmp.
- setUpdateTstmp(Date) - Method in class net.sourceforge.seqware.common.model.ShareProcessing
-
Setter for the field updateTstmp.
- setUpdateTstmp(Date) - Method in class net.sourceforge.seqware.common.model.ShareSample
-
Setter for the field updateTstmp.
- setUpdateValidator(Validator) - Method in class net.sourceforge.solexatools.webapp.controller.ExperimentController
-
Setter for the field updateValidator.
- setUpdateValidator(Validator) - Method in class net.sourceforge.solexatools.webapp.controller.StudyController
-
setUpdateValidator.
- setupDirectory() - Method in class net.sourceforge.seqware.pipeline.workflowV2.AbstractWorkflowDataModel
-
to be Overridden by the workflow author
- setupEnvironment() - Method in class net.sourceforge.seqware.pipeline.workflowV2.AbstractWorkflowDataModel
-
to be Overridden by the workflow author
generally people don't override this.
- setupFiles() - Method in class net.sourceforge.seqware.pipeline.workflowV2.AbstractWorkflowDataModel
-
to be Overridden by the workflow author
the place to specify inputs and outputs to the program
also, a user can specify inputs and outputs on jobs directly in which
case they are still provisioned properly with respect to the job (inputs before, outputs after)
when you define inputs/outputs here they are provisioned before all jobs
and after all jobs respectively
- setupWorkflow() - Method in class net.sourceforge.seqware.pipeline.workflowV2.AbstractWorkflowDataModel
-
to be Overridden by the workflow author
you generally don't call this as the workflow author since it promotes hardcoding
this will typically be filled in by maven
- setUrl(String) - Method in class io.seqware.webservice.generated.model.ExperimentLink
-
- setUrl(String) - Method in class io.seqware.webservice.generated.model.File
-
- setUrl(String) - Method in class io.seqware.webservice.generated.model.IusLink
-
- setUrl(String) - Method in class io.seqware.webservice.generated.model.LaneLink
-
- setUrl(String) - Method in class io.seqware.webservice.generated.model.Processing
-
- setUrl(String) - Method in class io.seqware.webservice.generated.model.ProcessingExperiments
-
- setUrl(String) - Method in class io.seqware.webservice.generated.model.ProcessingIus
-
- setUrl(String) - Method in class io.seqware.webservice.generated.model.ProcessingLanes
-
- setUrl(String) - Method in class io.seqware.webservice.generated.model.ProcessingSamples
-
- setUrl(String) - Method in class io.seqware.webservice.generated.model.ProcessingSequencerRuns
-
- setUrl(String) - Method in class io.seqware.webservice.generated.model.ProcessingStudies
-
- setUrl(String) - Method in class io.seqware.webservice.generated.model.SampleLink
-
- setUrl(String) - Method in class io.seqware.webservice.generated.model.StudyLink
-
- setUrl(String) - Method in class net.sourceforge.seqware.common.model.ExperimentLink
-
Setter for the field url.
- setUrl(String) - Method in class net.sourceforge.seqware.common.model.File
-
Setter for the field url.
- setUrl(String) - Method in class net.sourceforge.seqware.common.model.IUSLink
-
Setter for the field url.
- setUrl(String) - Method in class net.sourceforge.seqware.common.model.LaneLink
-
Setter for the field url.
- setUrl(String) - Method in class net.sourceforge.seqware.common.model.Processing
-
Setter for the field url.
- setUrl(String) - Method in class net.sourceforge.seqware.common.model.ProcessingExperiments
-
Setter for the field url.
- setUrl(String) - Method in class net.sourceforge.seqware.common.model.ProcessingIus
-
Setter for the field url.
- setUrl(String) - Method in class net.sourceforge.seqware.common.model.ProcessingLanes
-
Setter for the field url.
- setUrl(String) - Method in class net.sourceforge.seqware.common.model.ProcessingSamples
-
Setter for the field url.
- setUrl(String) - Method in class net.sourceforge.seqware.common.model.ProcessingSequencerRuns
-
Setter for the field url.
- setUrl(String) - Method in class net.sourceforge.seqware.common.model.ProcessingStudies
-
Setter for the field url.
- setUrl(String) - Method in class net.sourceforge.seqware.common.model.SampleLink
-
Setter for the field url.
- setUrl(String) - Method in class net.sourceforge.seqware.common.model.StudyLink
-
Setter for the field url.
- setUrl(String) - Method in class net.sourceforge.seqware.common.module.FileMetadata
-
- setUrl(String) - Method in class net.sourceforge.seqware.common.module.ReturnValue
-
Setter for the field url.
- setUrl(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object.Pfn
-
Setter for the field url.
- setUrl(String) - Method in class net.sourceforge.seqware.webservice.dto.AttributeDto
-
Setter for the field url.
- setUrl(String) - Method in class net.sourceforge.seqware.webservice.dto.FileDto
-
Setter for the field url.
- setUrl(String) - Method in class net.sourceforge.seqware.webservice.dto.IusDto
-
Setter for the field url.
- setUrl(String) - Method in class net.sourceforge.seqware.webservice.dto.LibraryDto
-
Setter for the field url.
- setUrl(String) - Method in class net.sourceforge.seqware.webservice.dto.SampleSearchDto
-
Setter for the field url.
- setUrlLabel(String) - Method in class io.seqware.webservice.generated.model.File
-
- setUrlLabel(String) - Method in class io.seqware.webservice.generated.model.Processing
-
- setUrlLabel(String) - Method in class net.sourceforge.seqware.common.model.File
-
Setter for the field urlLabel.
- setUrlLabel(String) - Method in class net.sourceforge.seqware.common.model.Processing
-
Setter for the field urlLabel.
- setUrlLabel(String) - Method in class net.sourceforge.seqware.common.module.FileMetadata
-
- setUrlLabel(String) - Method in class net.sourceforge.seqware.common.module.ReturnValue
-
Setter for the field urlLabel.
- setUseCheckFile(boolean) - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object.OozieJob
-
- setUseIparIntensities(Boolean) - Method in class io.seqware.webservice.generated.model.SequencerRun
-
- setUseIparIntensities(Boolean) - Method in class net.sourceforge.seqware.common.model.SequencerRun
-
Setter for the field useIparIntensities.
- setUseIparIntensities(Boolean) - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
-
Setter for the field useIparIntensities.
- setUseOneURL(Boolean) - Method in class net.sourceforge.seqware.common.model.UploadSequence
-
Setter for the field useOneURL.
- setUserMl(boolean) - Method in class io.seqware.webservice.generated.model.Registration
-
- setUsername(String) - Method in class io.seqware.webservice.generated.model.Workflow
-
- setUsername(String) - Method in class io.seqware.webservice.generated.model.WorkflowRun
-
- setUsername(String) - Method in class net.sourceforge.seqware.common.model.Workflow
-
Setter for the field username.
- setUserName(String) - Method in class net.sourceforge.seqware.common.model.WorkflowRun
-
Setter for the field userName.
- setUseTwoURL(Boolean) - Method in class net.sourceforge.seqware.common.model.UploadSequence
-
Setter for the field useTwoURL.
- setUseURL(Boolean) - Method in class net.sourceforge.seqware.common.business.UploadFile
-
Setter for the field useURL.
- setValidationReportService(ValidationReportService) - Method in class net.sourceforge.seqware.common.ContextImpl
-
Setter for the field validationReportService.
- setValidator(Validator) - Method in class net.sourceforge.solexatools.webapp.controller.ExperimentController
-
Setter for the field validator.
- setValidator(Validator) - Method in class net.sourceforge.solexatools.webapp.controller.FileController
-
Setter for the field validator.
- setValidator(Validator) - Method in class net.sourceforge.solexatools.webapp.controller.LaneController
-
Setter for the field validator.
- setValidator(Validator) - Method in class net.sourceforge.solexatools.webapp.controller.ProcessingController
-
Setter for the field validator.
- setValidator(Validator) - Method in class net.sourceforge.solexatools.webapp.controller.RegistrationController
-
Setter for the field validator.
- setValidator(Validator) - Method in class net.sourceforge.solexatools.webapp.controller.SampleController
-
Setter for the field validator.
- setValidator(Validator) - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunController
-
Setter for the field validator.
- setValidator(Validator) - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunControllerDTO
-
Setter for the field validator.
- setValidator(Validator) - Method in class net.sourceforge.solexatools.webapp.controller.StudyController
-
setValidator.
- setValidator(Validator) - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileController
-
Setter for the field validator.
- setValidator(Validator) - Method in class net.sourceforge.solexatools.webapp.controller.UploadSequenceController
-
Setter for the field validator.
- setValidator(Validator) - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowController
-
Setter for the field validator.
- setValidator(Validator) - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowParamController
-
Setter for the field validator.
- setValidator(Validator) - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowParamValueController
-
Setter for the field validator.
- setValidator(Validator) - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowRunController
-
Setter for the field validator.
- setValue(String) - Method in class io.seqware.webservice.generated.model.ExpenseAttribute
-
- setValue(String) - Method in class io.seqware.webservice.generated.model.ExperimentAttribute
-
- setValue(String) - Method in class io.seqware.webservice.generated.model.FileAttribute
-
- setValue(String) - Method in class io.seqware.webservice.generated.model.InvoiceAttribute
-
- setValue(String) - Method in class io.seqware.webservice.generated.model.IusAttribute
-
- setValue(String) - Method in class io.seqware.webservice.generated.model.LaneAttribute
-
- setValue(String) - Method in class io.seqware.webservice.generated.model.ProcessingAttribute
-
- setValue(String) - Method in class io.seqware.webservice.generated.model.SampleAttribute
-
- setValue(String) - Method in class io.seqware.webservice.generated.model.SampleSearchAttribute
-
- setValue(String) - Method in class io.seqware.webservice.generated.model.SequencerRunAttribute
-
- setValue(String) - Method in class io.seqware.webservice.generated.model.StudyAttribute
-
- setValue(String) - Method in class io.seqware.webservice.generated.model.WorkflowAttribute
-
- setValue(String) - Method in class io.seqware.webservice.generated.model.WorkflowParamValue
-
- setValue(String) - Method in class io.seqware.webservice.generated.model.WorkflowRunAttribute
-
- setValue(String) - Method in class io.seqware.webservice.generated.model.WorkflowRunParam
-
- setValue(String) - Method in interface net.sourceforge.seqware.common.model.Attribute
-
setValue.
- setValue(String) - Method in class net.sourceforge.seqware.common.model.ExperimentAttribute
-
Setter for the field value.
- setValue(String) - Method in class net.sourceforge.seqware.common.model.FileAttribute
-
setValue.
- setValue(String) - Method in class net.sourceforge.seqware.common.model.IUSAttribute
-
setValue.
- setValue(String) - Method in class net.sourceforge.seqware.common.model.LaneAttribute
-
Setter for the field value.
- setValue(String) - Method in class net.sourceforge.seqware.common.model.ProcessingAttribute
-
setValue.
- setValue(String) - Method in class net.sourceforge.seqware.common.model.SampleAttribute
-
setValue.
- setValue(String) - Method in class net.sourceforge.seqware.common.model.SampleSearchAttribute
-
setValue.
- setValue(String) - Method in class net.sourceforge.seqware.common.model.SequencerRunAttribute
-
setValue.
- setValue(String) - Method in class net.sourceforge.seqware.common.model.StudyAttribute
-
setValue.
- setValue(String) - Method in class net.sourceforge.seqware.common.model.WorkflowAttribute
-
setValue.
- setValue(String) - Method in class net.sourceforge.seqware.common.model.WorkflowParam
-
Setter for the field value.
- setValue(String) - Method in class net.sourceforge.seqware.common.model.WorkflowParamValue
-
Setter for the field value.
- setValue(String) - Method in class net.sourceforge.seqware.common.model.WorkflowRunAttribute
-
setValue.
- setValue(String) - Method in class net.sourceforge.seqware.common.model.WorkflowRunParam
-
Setter for the field value.
- setValue(String) - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.TagValueUnit
-
- setValue(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Argument
-
Setter for the field value.
- setValue(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.JobProfile
-
Setter for the field value.
- setValue(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Requirement
-
- setValue(String) - Method in class net.sourceforge.seqware.webservice.dto.AttributeDto
-
Setter for the field value.
- setValues(SortedSet<WorkflowParamValue>) - Method in class net.sourceforge.seqware.common.model.WorkflowParam
-
Setter for the field values.
- setVerbose(boolean) - Method in class net.sourceforge.seqware.common.util.filetools.ProvisionFilesUtil
-
Enable class verbose mode.
- setVerbose(boolean) - Static method in class net.sourceforge.seqware.common.util.Log
-
override the log4j.properties
- setVersion(String) - Method in class io.seqware.webservice.generated.model.Processing
-
- setVersion(String) - Method in class io.seqware.webservice.generated.model.Workflow
-
- setVersion(String) - Method in class net.sourceforge.seqware.common.model.Processing
-
Setter for the field version.
- setVersion(String) - Method in class net.sourceforge.seqware.common.model.Workflow
-
Setter for the field version.
- setVersion(String) - Method in class net.sourceforge.seqware.common.module.ReturnValue
-
Setter for the field version.
- setVersion(String) - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowInfo
-
Setter for the field version.
- setVersion(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.AbstractWorkflowDataModel
-
set workflow version
- setVersion(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object.WorkflowExecutable
-
- setVisibleParams(SortedSet<WorkflowParam>) - Method in class net.sourceforge.solexatools.util.SummaryData
-
Setter for the field visibleParams.
- setWait(boolean) - Method in class net.sourceforge.seqware.pipeline.workflowV2.AbstractWorkflowDataModel
-
wait for the workflow to finished, user can override this by using --wait from command line
- setWebResource(WebResource) - Method in class io.seqware.webservice.generated.client.SeqWareWebserviceClient
-
- setWfRuns(WorkflowRun[]) - Method in class net.sourceforge.solexatools.webapp.metamodel.StudySampleReportLineItem
-
Setter for the field wfRuns.
- setWidth(int) - Method in class net.sourceforge.solexatools.webapp.metamodel.Flexigrid.ColumnModel
-
- setWithHasFile(SortedSet<Experiment>) - Method in interface net.sourceforge.seqware.common.business.ExperimentService
-
setWithHasFile.
- setWithHasFile(Set<File>, String) - Method in interface net.sourceforge.seqware.common.business.FileService
-
setWithHasFile.
- setWithHasFile(SortedSet<Experiment>) - Method in class net.sourceforge.seqware.common.business.impl.ExperimentServiceImpl
-
setWithHasFile.
- setWithHasFile(Set<File>, String) - Method in class net.sourceforge.seqware.common.business.impl.FileServiceImpl
-
setWithHasFile.
- setWithHasFile(SortedSet<IUS>) - Method in class net.sourceforge.seqware.common.business.impl.IUSServiceImpl
-
setWithHasFile.
- setWithHasFile(SortedSet<Lane>) - Method in class net.sourceforge.seqware.common.business.impl.LaneServiceImpl
-
setWithHasFile.
- setWithHasFile(Set<Processing>) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingServiceImpl
-
setWithHasFile.
- setWithHasFile(Set<Processing>, String) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingServiceImpl
-
setWithHasFile.
- setWithHasFile(Integer, SortedSet<Sample>) - Method in class net.sourceforge.seqware.common.business.impl.SampleServiceImpl
-
setWithHasFile.
- setWithHasFile(SortedSet<IUS>) - Method in interface net.sourceforge.seqware.common.business.IUSService
-
setWithHasFile.
- setWithHasFile(SortedSet<Lane>) - Method in interface net.sourceforge.seqware.common.business.LaneService
-
setWithHasFile.
- setWithHasFile(Set<Processing>) - Method in interface net.sourceforge.seqware.common.business.ProcessingService
-
setWithHasFile.
- setWithHasFile(Set<Processing>, String) - Method in interface net.sourceforge.seqware.common.business.ProcessingService
-
setWithHasFile.
- setWithHasFile(Integer, SortedSet<Sample>) - Method in interface net.sourceforge.seqware.common.business.SampleService
-
setWithHasFile.
- setWorkflow(Workflow) - Method in class net.sourceforge.seqware.common.model.SampleReportRow
-
Setter for the field workflow.
- setWorkflow(Workflow) - Method in class net.sourceforge.seqware.common.model.WorkflowAttribute
-
Setter for the field workflow.
- setWorkflow(Workflow) - Method in class net.sourceforge.seqware.common.model.WorkflowParam
-
Setter for the field workflow.
- setWorkflow(Workflow) - Method in class net.sourceforge.seqware.common.model.WorkflowRun
-
Setter for the field workflow.
- setWorkflow_engine(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.AbstractWorkflowDataModel
-
default is pegasus
- setWorkflowAccession(Integer) - Method in class net.sourceforge.seqware.common.model.WorkflowRun
-
- setWorkflowAccession(int) - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowInfo
-
Setter for the field workflowAccession.
- setWorkflowAccession(String) - Method in class net.sourceforge.seqware.pipeline.deciders.BasicDecider
-
- setWorkflowAccessionsToCheck(Set<String>) - Method in class net.sourceforge.seqware.pipeline.deciders.BasicDecider
-
- setWorkflowAttributeCollection(Collection<WorkflowAttribute>) - Method in class io.seqware.webservice.generated.model.Workflow
-
- setWorkflowAttributeId(Integer) - Method in class io.seqware.webservice.generated.model.WorkflowAttribute
-
- setWorkflowAttributes(Set<WorkflowAttribute>) - Method in class net.sourceforge.seqware.common.model.Workflow
-
Setter for the field workflowAttributes.
- setWorkflowBundleDir(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.AbstractWorkflowDataModel
-
- setWorkflowBundleDir(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Workflow
-
set the workflowBundle directory
- setWorkflowClass(String) - Method in class io.seqware.webservice.generated.model.Workflow
-
- setWorkflowClass(String) - Method in class net.sourceforge.seqware.common.model.Workflow
-
- setWorkflowClass(String) - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowInfo
-
- setWorkflowCollection(Collection<Workflow>) - Method in class io.seqware.webservice.generated.model.Registration
-
- setWorkflowDAO(WorkflowDAO) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowServiceImpl
-
setWorkflowDAO.
- setWorkflowDAO(WorkflowDAO) - Method in interface net.sourceforge.seqware.common.business.WorkflowService
-
setWorkflowDAO.
- setWorkflowDir(String) - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowInfo
-
Setter for the field workflowDir.
- setWorkflowEngine(String) - Method in class io.seqware.webservice.generated.model.Workflow
-
- setWorkflowEngine(String) - Method in class io.seqware.webservice.generated.model.WorkflowRun
-
- setWorkflowEngine(String) - Method in class net.sourceforge.seqware.common.model.Workflow
-
- setWorkflowEngine(String) - Method in class net.sourceforge.seqware.common.model.WorkflowRun
-
- setWorkflowEngine(String) - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowInfo
-
- setWorkflowId(Integer) - Method in class io.seqware.webservice.generated.model.SampleReport
-
- setWorkflowId(Integer) - Method in class io.seqware.webservice.generated.model.Workflow
-
- setWorkflowId(Workflow) - Method in class io.seqware.webservice.generated.model.WorkflowAttribute
-
- setWorkflowId(Workflow) - Method in class io.seqware.webservice.generated.model.WorkflowParam
-
- setWorkflowId(Workflow) - Method in class io.seqware.webservice.generated.model.WorkflowRun
-
- setWorkflowId(Integer) - Method in class net.sourceforge.seqware.common.model.Workflow
-
Setter for the field workflowId.
- setWorkflowParam(WorkflowParam) - Method in class net.sourceforge.seqware.common.model.WorkflowParamValue
-
Setter for the field workflowParam.
- setWorkflowParamCollection(Collection<WorkflowParam>) - Method in class io.seqware.webservice.generated.model.Workflow
-
- setWorkflowParamDAO(WorkflowParamDAO) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowParamServiceImpl
-
setWorkflowParamDAO.
- setWorkflowParamDAO(WorkflowParamDAO) - Method in interface net.sourceforge.seqware.common.business.WorkflowParamService
-
setWorkflowParamDAO.
- setWorkflowParamId(Integer) - Method in class io.seqware.webservice.generated.model.WorkflowParam
-
- setWorkflowParamId(WorkflowParam) - Method in class io.seqware.webservice.generated.model.WorkflowParamValue
-
- setWorkflowParamId(Integer) - Method in class net.sourceforge.seqware.common.model.WorkflowParam
-
Setter for the field workflowParamId.
- setWorkflowParamId(Integer) - Method in class net.sourceforge.seqware.common.model.WorkflowParamValue
-
Setter for the field workflowParamId.
- setWorkflowParams(SortedSet<WorkflowParam>) - Method in class net.sourceforge.seqware.common.model.Workflow
-
Setter for the field workflowParams.
- setWorkflowParamService(WorkflowParamService) - Method in class net.sourceforge.seqware.common.ContextImpl
-
Setter for the field workflowParamService.
- setWorkflowParamService(WorkflowParamService) - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowParamController
-
Setter for the field workflowParamService.
- setWorkflowParamService(WorkflowParamService) - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowParamSetupController
-
Setter for the field workflowParamService.
- setWorkflowParamService(WorkflowParamService) - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowParamValueSetupController
-
Setter for the field workflowParamService.
- setWorkflowParamValueCollection(Collection<WorkflowParamValue>) - Method in class io.seqware.webservice.generated.model.WorkflowParam
-
- setWorkflowParamValueDAO(WorkflowParamValueDAO) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowParamValueServiceImpl
-
setWorkflowParamValueDAO.
- setWorkflowParamValueDAO(WorkflowParamValueDAO) - Method in interface net.sourceforge.seqware.common.business.WorkflowParamValueService
-
setWorkflowParamValueDAO.
- setWorkflowParamValueId(Integer) - Method in class io.seqware.webservice.generated.model.WorkflowParamValue
-
- setWorkflowParamValueId(Integer) - Method in class net.sourceforge.seqware.common.model.WorkflowParamValue
-
Setter for the field workflowParamValueId.
- setWorkflowParamValueService(WorkflowParamValueService) - Method in class net.sourceforge.seqware.common.ContextImpl
-
Setter for the field workflowParamValueService.
- setWorkflowParamValueService(WorkflowParamValueService) - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowParamValueController
-
Setter for the field workflowParamValueService.
- setWorkflowParamValueService(WorkflowParamValueService) - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowParamValueSetupController
-
Setter for the field workflowParamValueService.
- setWorkflowRun(WorkflowRun) - Method in class net.sourceforge.seqware.common.hibernate.reports.WorkflowRunReportRow
-
Setter for the field workflowRun.
- setWorkflowRun(WorkflowRun) - Method in class net.sourceforge.seqware.common.model.Expense
-
Setter for the field
workflowRun.
- setWorkflowRun(WorkflowRun) - Method in class net.sourceforge.seqware.common.model.Processing
-
Setter for the field workflowRun.
- setWorkflowRun(WorkflowRun) - Method in class net.sourceforge.seqware.common.model.WorkflowRunAttribute
-
Setter for the field workflowRun.
- setWorkflowRun(WorkflowRun) - Method in class net.sourceforge.seqware.common.model.WorkflowRunParam
-
Setter for the field workflowRun.
- setWorkflowRun(Integer, HttpServletRequest) - Static method in class net.sourceforge.solexatools.util.SetNodeIdInSession
-
setWorkflowRun.
- setWorkflowRunAccession(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object.OozieJob
-
- setWorkflowRunAccession(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object.PegasusJob
-
- setWorkflowRunAncesstor(boolean) - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object.OozieJob
-
- setWorkflowRunAncesstor(boolean) - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object.PegasusJob
-
- setWorkflowRunAttributeCollection(Collection<WorkflowRunAttribute>) - Method in class io.seqware.webservice.generated.model.WorkflowRun
-
- setWorkflowRunAttributeId(Integer) - Method in class io.seqware.webservice.generated.model.WorkflowRunAttribute
-
- setWorkflowRunAttributes(Set<WorkflowRunAttribute>) - Method in class net.sourceforge.seqware.common.model.WorkflowRun
-
Setter for the field workflowRunAttributes.
- setWorkflowRunByAncestorWorkflowRunId(WorkflowRun) - Method in class net.sourceforge.seqware.common.model.Processing
-
Setter for the field workflowRunByAncestorWorkflowRunId.
- setWorkflowRunCollection(Collection<WorkflowRun>) - Method in class io.seqware.webservice.generated.model.File
-
- setWorkflowRunCollection(Collection<WorkflowRun>) - Method in class io.seqware.webservice.generated.model.Registration
-
- setWorkflowRunCollection(Collection<WorkflowRun>) - Method in class io.seqware.webservice.generated.model.Workflow
-
- setWorkflowRunDAO(WorkflowRunDAO) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowRunServiceImpl
-
setWorkflowRunDAO.
- setWorkflowRunDAO(WorkflowRunDAO) - Method in interface net.sourceforge.seqware.common.business.WorkflowRunService
-
setWorkflowRunDAO.
- setWorkflowRunId(Integer) - Method in class io.seqware.webservice.generated.model.Expense
-
- setWorkflowRunId(WorkflowRun) - Method in class io.seqware.webservice.generated.model.IusWorkflowRuns
-
- setWorkflowRunId(WorkflowRun) - Method in class io.seqware.webservice.generated.model.LaneWorkflowRuns
-
- setWorkflowRunId(WorkflowRun) - Method in class io.seqware.webservice.generated.model.Processing
-
- setWorkflowRunId(WorkflowRun) - Method in class io.seqware.webservice.generated.model.ShareWorkflowRun
-
- setWorkflowRunId(Integer) - Method in class io.seqware.webservice.generated.model.WorkflowRun
-
- setWorkflowRunId(WorkflowRun) - Method in class io.seqware.webservice.generated.model.WorkflowRunAttribute
-
- setWorkflowRunId(WorkflowRun) - Method in class io.seqware.webservice.generated.model.WorkflowRunParam
-
- setWorkflowRunId(Integer) - Method in class net.sourceforge.seqware.common.model.Processing
-
Setter for the field workflowRunId.
- setWorkflowRunId(Integer) - Method in class net.sourceforge.seqware.common.model.ShareWorkflowRun
-
Setter for the field workflowRunId.
- setWorkflowRunId(Integer) - Method in class net.sourceforge.seqware.common.model.WorkflowRun
-
Setter for the field workflowRunId.
- setWorkflowRunParamCollection(Collection<WorkflowRunParam>) - Method in class io.seqware.webservice.generated.model.WorkflowRun
-
- setWorkflowRunParamDAO(WorkflowRunParamDAO) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowRunParamServiceImpl
-
setWorkflowRunParamDAO.
- setWorkflowRunParamDAO(WorkflowRunParamDAO) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowRunServiceImpl
-
Setter for the field workflowRunParamDAO.
- setWorkflowRunParamDAO(WorkflowRunParamDAO) - Method in interface net.sourceforge.seqware.common.business.WorkflowRunParamService
-
setWorkflowRunParamDAO.
- setWorkflowRunParamId(Integer) - Method in class io.seqware.webservice.generated.model.WorkflowRunParam
-
- setWorkflowRunParamId(Integer) - Method in class net.sourceforge.seqware.common.model.WorkflowRunParam
-
setWorkflowRunParamId.
- setWorkflowRunParams(SortedSet<WorkflowRunParam>) - Method in class net.sourceforge.seqware.common.model.WorkflowRun
-
Setter for the field workflowRunParams.
- setWorkflowRunProcessings(Collection<Processing>) - Method in class net.sourceforge.seqware.common.hibernate.reports.WorkflowRunReportRow
-
Setter for the field workflowRunProcessings.
- setWorkflowRunRunning(Integer, HttpServletRequest) - Static method in class net.sourceforge.solexatools.util.SetNodeIdInSession
-
setWorkflowRunRunning.
- setWorkflowRunRunningWithSample(HttpServletRequest) - Static method in class net.sourceforge.solexatools.util.SetNodeIdInSession
-
setWorkflowRunRunningWithSample.
- setWorkflowRuns(Set<WorkflowRun>) - Method in class net.sourceforge.seqware.common.model.IUS
-
Setter for the field workflowRuns.
- setWorkflowRuns(Set<WorkflowRun>) - Method in class net.sourceforge.seqware.common.model.Lane
-
Setter for the field workflowRuns.
- setWorkflowRuns(SortedSet<WorkflowRun>) - Method in class net.sourceforge.seqware.common.model.Workflow
-
Setter for the field workflowRuns.
- setWorkflowRunService(WorkflowRunService) - Method in class net.sourceforge.seqware.common.ContextImpl
-
Setter for the field workflowRunService.
- setWorkflowRunService(WorkflowRunService) - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysBulkDownloadListController
-
Setter for the field workflowRunService.
- setWorkflowRunService(WorkflowRunService) - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysBulkDownloadListDetailsController
-
Setter for the field workflowRunService.
- setWorkflowRunService(WorkflowRunService) - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysEventController
-
Setter for the field workflowRunService.
- setWorkflowRunService(WorkflowRunService) - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysListController
-
Setter for the field workflowRunService.
- setWorkflowRunService(WorkflowRunService) - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysListDetailsController
-
Setter for the field workflowRunService.
- setWorkflowRunService(WorkflowRunService) - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysRunningListDetailsController
-
Setter for the field workflowRunService.
- setWorkflowRunService(WorkflowRunService) - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysTableController
-
Setter for the field
workflowRunService.
- setWorkflowRunService(WorkflowRunService) - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysTableControllerDetails
-
Setter for the field
workflowRunService.
- setWorkflowRunService(WorkflowRunService) - Method in class net.sourceforge.solexatools.webapp.controller.CancelAnalysisWorkflowController
-
Setter for the field workflowRunService.
- setWorkflowRunService(WorkflowRunService) - Method in class net.sourceforge.solexatools.webapp.controller.DownloadFileListController
-
Setter for the field workflowRunService.
- setWorkflowRunService(WorkflowRunService) - Method in class net.sourceforge.solexatools.webapp.controller.EntityController
-
Setter for the field workflowRunService.
- setWorkflowRunService(WorkflowRunService) - Method in class net.sourceforge.solexatools.webapp.controller.LaunchWorkflowController
-
Setter for the field workflowRunService.
- setWorkflowRunService(WorkflowRunService) - Method in class net.sourceforge.solexatools.webapp.controller.RetryAnalysisWorkflowController
-
Setter for the field workflowRunService.
- setWorkflowRunService(WorkflowRunService) - Method in class net.sourceforge.solexatools.webapp.controller.SampleWorkflowRunsController
-
Setter for the field workflowRunService.
- setWorkflowRunService(WorkflowRunService) - Method in class net.sourceforge.solexatools.webapp.controller.SearchResultsListController
-
Setter for the field workflowRunService.
- setWorkflowRunService(WorkflowRunService) - Method in class net.sourceforge.solexatools.webapp.controller.SelectInputController
-
Setter for the field workflowRunService.
- setWorkflowRunService(WorkflowRunService) - Method in class net.sourceforge.solexatools.webapp.controller.SelectInputListController
-
Setter for the field workflowRunService.
- setWorkflowRunService(WorkflowRunService) - Method in class net.sourceforge.solexatools.webapp.controller.ShareValidatorController
-
Setter for the field workflowRunService.
- setWorkflowRunService(WorkflowRunService) - Method in class net.sourceforge.solexatools.webapp.controller.StudyListDetailsFlatController
-
Setter for the field workflowRunService.
- setWorkflowRunService(WorkflowRunService) - Method in class net.sourceforge.solexatools.webapp.controller.SummaryLaunchWorkflowController
-
Setter for the field workflowRunService.
- setWorkflowRunService(WorkflowRunService) - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowRunSetupController
-
Setter for the field workflowRunService.
- setWorkflowRunWithSample(HttpServletRequest) - Static method in class net.sourceforge.solexatools.util.SetNodeIdInSession
-
setWorkflowRunWithSample.
- setWorkflows(ArrayList<WorkflowInfo>) - Method in class net.sourceforge.seqware.pipeline.bundle.BundleInfo
-
Setter for the field workflows.
- setWorkflowService(WorkflowService) - Method in class net.sourceforge.seqware.common.ContextImpl
-
Setter for the field workflowService.
- setWorkflowService(WorkflowService) - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysListController
-
Setter for the field workflowService.
- setWorkflowService(WorkflowService) - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysTableController
-
Setter for the field
workflowService.
- setWorkflowService(WorkflowService) - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysTableControllerDetails
-
Setter for the field
workflowService.
- setWorkflowService(WorkflowService) - Method in class net.sourceforge.solexatools.webapp.controller.ChangeWorkflowParamValueController
-
Setter for the field workflowService.
- setWorkflowService(WorkflowService) - Method in class net.sourceforge.solexatools.webapp.controller.EntityController
-
Setter for the field workflowService.
- setWorkflowService(WorkflowService) - Method in class net.sourceforge.solexatools.webapp.controller.LaunchWorkflowController
-
Setter for the field workflowService.
- setWorkflowService(WorkflowService) - Method in class net.sourceforge.solexatools.webapp.controller.LaunchWorkflowSetupController
-
Setter for the field workflowService.
- setWorkflowService(WorkflowService) - Method in class net.sourceforge.solexatools.webapp.controller.ManageWorkflowsController
-
Setter for the field workflowService.
- setWorkflowService(WorkflowService) - Method in class net.sourceforge.solexatools.webapp.controller.SearchResultsListController
-
Setter for the field workflowService.
- setWorkflowService(WorkflowService) - Method in class net.sourceforge.solexatools.webapp.controller.SelectInputController
-
Setter for the field workflowService.
- setWorkflowService(WorkflowService) - Method in class net.sourceforge.solexatools.webapp.controller.SummaryLaunchWorkflowController
-
Setter for the field workflowService.
- setWorkflowService(WorkflowService) - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowController
-
Setter for the field workflowService.
- setWorkflowService(WorkflowService) - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowListSetupController
-
Setter for the field workflowService.
- setWorkflowService(WorkflowService) - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowParamListController
-
Setter for the field workflowService.
- setWorkflowService(WorkflowService) - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowSetupController
-
Setter for the field workflowService.
- setWorkflowSqwVersion(String) - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowInfo
-
setWorkflowSqwVersion.
- setWorkflowTemplate(String) - Method in class io.seqware.webservice.generated.model.Workflow
-
- setWorkflowTemplate(String) - Method in class io.seqware.webservice.generated.model.WorkflowRun
-
- setWorkflowType(String) - Method in class io.seqware.webservice.generated.model.Workflow
-
- setWorkflowType(String) - Method in class net.sourceforge.seqware.common.model.Workflow
-
- setWorkflowType(String) - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowInfo
-
- setWorkflowType(String) - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.RunInfo
-
Set the value of workflowType
- SGE_MAX_MEMORY_PARAM_VARIABLE - Static variable in class net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object.OozieJob
-
Variable identifier to be used within the qsub max-memory parameter to
specify the value.
- SGE_THREADS_PARAM_VARIABLE - Static variable in class net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object.OozieJob
-
Variable identifier to be used within the qsub threads parameter to specify
the value.
- SGE_XMLNS - Static variable in class net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object.OozieJob
-
Namespace of the Oozie SGE action xml node.
- ShareExperiment - Class in io.seqware.webservice.generated.model
-
- ShareExperiment() - Constructor for class io.seqware.webservice.generated.model.ShareExperiment
-
- ShareExperiment(Integer) - Constructor for class io.seqware.webservice.generated.model.ShareExperiment
-
- ShareExperiment(Integer, Date) - Constructor for class io.seqware.webservice.generated.model.ShareExperiment
-
- ShareExperiment - Class in net.sourceforge.seqware.common.model
-
ShareExperiment generated by hbm2java
- ShareExperiment() - Constructor for class net.sourceforge.seqware.common.model.ShareExperiment
-
Constructor for ShareExperiment.
- ShareExperiment(int, Experiment, Registration, Date) - Constructor for class net.sourceforge.seqware.common.model.ShareExperiment
-
Constructor for ShareExperiment.
- ShareExperiment(int, Experiment, Registration, Boolean, Integer, Date, Date) - Constructor for class net.sourceforge.seqware.common.model.ShareExperiment
-
Constructor for ShareExperiment.
- ShareExperimentDAO - Interface in net.sourceforge.seqware.common.dao
-
ShareExperimentDAO interface.
- ShareExperimentDAOHibernate - Class in net.sourceforge.seqware.common.dao.hibernate
-
ShareExperimentDAOHibernate class.
- ShareExperimentDAOHibernate() - Constructor for class net.sourceforge.seqware.common.dao.hibernate.ShareExperimentDAOHibernate
-
- ShareExperimentFacadeREST - Class in io.seqware.webservice.generated.controller
-
- ShareExperimentFacadeREST() - Constructor for class io.seqware.webservice.generated.controller.ShareExperimentFacadeREST
-
- ShareExperimentService - Interface in net.sourceforge.seqware.common.business
-
ShareExperimentService interface.
- ShareExperimentServiceImpl - Class in net.sourceforge.seqware.common.business.impl
-
ShareExperimentServiceImpl class.
- ShareExperimentServiceImpl() - Constructor for class net.sourceforge.seqware.common.business.impl.ShareExperimentServiceImpl
-
- ShareFile - Class in io.seqware.webservice.generated.model
-
- ShareFile() - Constructor for class io.seqware.webservice.generated.model.ShareFile
-
- ShareFile(Integer) - Constructor for class io.seqware.webservice.generated.model.ShareFile
-
- ShareFile(Integer, Date) - Constructor for class io.seqware.webservice.generated.model.ShareFile
-
- ShareFile - Class in net.sourceforge.seqware.common.model
-
ShareFile generated by hbm2java
- ShareFile() - Constructor for class net.sourceforge.seqware.common.model.ShareFile
-
Constructor for ShareFile.
- ShareFile(int, File, Registration, Date) - Constructor for class net.sourceforge.seqware.common.model.ShareFile
-
Constructor for ShareFile.
- ShareFile(int, File, Registration, Boolean, Integer, Date, Date) - Constructor for class net.sourceforge.seqware.common.model.ShareFile
-
Constructor for ShareFile.
- ShareFileDAO - Interface in net.sourceforge.seqware.common.dao
-
ShareFileDAO interface.
- ShareFileDAOHibernate - Class in net.sourceforge.seqware.common.dao.hibernate
-
ShareFileDAOHibernate class.
- ShareFileDAOHibernate() - Constructor for class net.sourceforge.seqware.common.dao.hibernate.ShareFileDAOHibernate
-
- ShareFileFacadeREST - Class in io.seqware.webservice.generated.controller
-
- ShareFileFacadeREST() - Constructor for class io.seqware.webservice.generated.controller.ShareFileFacadeREST
-
- ShareFileService - Interface in net.sourceforge.seqware.common.business
-
ShareFileService interface.
- ShareFileServiceImpl - Class in net.sourceforge.seqware.common.business.impl
-
ShareFileServiceImpl class.
- ShareFileServiceImpl() - Constructor for class net.sourceforge.seqware.common.business.impl.ShareFileServiceImpl
-
- ShareLane - Class in io.seqware.webservice.generated.model
-
- ShareLane() - Constructor for class io.seqware.webservice.generated.model.ShareLane
-
- ShareLane(Integer) - Constructor for class io.seqware.webservice.generated.model.ShareLane
-
- ShareLane(Integer, Date) - Constructor for class io.seqware.webservice.generated.model.ShareLane
-
- ShareLane - Class in net.sourceforge.seqware.common.model
-
ShareLane generated by hbm2java
- ShareLane() - Constructor for class net.sourceforge.seqware.common.model.ShareLane
-
Constructor for ShareLane.
- ShareLane(int, Lane, Registration, Date) - Constructor for class net.sourceforge.seqware.common.model.ShareLane
-
Constructor for ShareLane.
- ShareLane(int, Lane, Registration, Boolean, Integer, Date, Date) - Constructor for class net.sourceforge.seqware.common.model.ShareLane
-
Constructor for ShareLane.
- ShareLaneDAO - Interface in net.sourceforge.seqware.common.dao
-
ShareLaneDAO interface.
- ShareLaneDAOHibernate - Class in net.sourceforge.seqware.common.dao.hibernate
-
ShareLaneDAOHibernate class.
- ShareLaneDAOHibernate() - Constructor for class net.sourceforge.seqware.common.dao.hibernate.ShareLaneDAOHibernate
-
- ShareLaneFacadeREST - Class in io.seqware.webservice.generated.controller
-
- ShareLaneFacadeREST() - Constructor for class io.seqware.webservice.generated.controller.ShareLaneFacadeREST
-
- ShareLaneService - Interface in net.sourceforge.seqware.common.business
-
ShareLaneService interface.
- ShareLaneServiceImpl - Class in net.sourceforge.seqware.common.business.impl
-
ShareLaneServiceImpl class.
- ShareLaneServiceImpl() - Constructor for class net.sourceforge.seqware.common.business.impl.ShareLaneServiceImpl
-
- ShareProcessing - Class in io.seqware.webservice.generated.model
-
- ShareProcessing() - Constructor for class io.seqware.webservice.generated.model.ShareProcessing
-
- ShareProcessing(Integer) - Constructor for class io.seqware.webservice.generated.model.ShareProcessing
-
- ShareProcessing(Integer, Date) - Constructor for class io.seqware.webservice.generated.model.ShareProcessing
-
- ShareProcessing - Class in net.sourceforge.seqware.common.model
-
ShareProcessing generated by hbm2java
- ShareProcessing() - Constructor for class net.sourceforge.seqware.common.model.ShareProcessing
-
Constructor for ShareProcessing.
- ShareProcessing(int, Processing, Registration, Date) - Constructor for class net.sourceforge.seqware.common.model.ShareProcessing
-
Constructor for ShareProcessing.
- ShareProcessing(int, Processing, Registration, Boolean, Integer, Date, Date) - Constructor for class net.sourceforge.seqware.common.model.ShareProcessing
-
Constructor for ShareProcessing.
- ShareProcessingDAO - Interface in net.sourceforge.seqware.common.dao
-
ShareProcessingDAO interface.
- ShareProcessingDAOHibernate - Class in net.sourceforge.seqware.common.dao.hibernate
-
ShareProcessingDAOHibernate class.
- ShareProcessingDAOHibernate() - Constructor for class net.sourceforge.seqware.common.dao.hibernate.ShareProcessingDAOHibernate
-
- ShareProcessingFacadeREST - Class in io.seqware.webservice.generated.controller
-
- ShareProcessingFacadeREST() - Constructor for class io.seqware.webservice.generated.controller.ShareProcessingFacadeREST
-
- ShareProcessingService - Interface in net.sourceforge.seqware.common.business
-
ShareProcessingService interface.
- ShareProcessingServiceImpl - Class in net.sourceforge.seqware.common.business.impl
-
ShareProcessingServiceImpl class.
- ShareProcessingServiceImpl() - Constructor for class net.sourceforge.seqware.common.business.impl.ShareProcessingServiceImpl
-
- ShareSample - Class in io.seqware.webservice.generated.model
-
- ShareSample() - Constructor for class io.seqware.webservice.generated.model.ShareSample
-
- ShareSample(Integer) - Constructor for class io.seqware.webservice.generated.model.ShareSample
-
- ShareSample(Integer, Date) - Constructor for class io.seqware.webservice.generated.model.ShareSample
-
- ShareSample - Class in net.sourceforge.seqware.common.model
-
ShareSample generated by hbm2java
- ShareSample() - Constructor for class net.sourceforge.seqware.common.model.ShareSample
-
Constructor for ShareSample.
- ShareSample(int, Sample, Registration, Date) - Constructor for class net.sourceforge.seqware.common.model.ShareSample
-
Constructor for ShareSample.
- ShareSample(int, Sample, Registration, Boolean, Integer, Date, Date) - Constructor for class net.sourceforge.seqware.common.model.ShareSample
-
Constructor for ShareSample.
- ShareSampleDAO - Interface in net.sourceforge.seqware.common.dao
-
ShareSampleDAO interface.
- ShareSampleDAOHibernate - Class in net.sourceforge.seqware.common.dao.hibernate
-
ShareSampleDAOHibernate class.
- ShareSampleDAOHibernate() - Constructor for class net.sourceforge.seqware.common.dao.hibernate.ShareSampleDAOHibernate
-
- ShareSampleFacadeREST - Class in io.seqware.webservice.generated.controller
-
- ShareSampleFacadeREST() - Constructor for class io.seqware.webservice.generated.controller.ShareSampleFacadeREST
-
- ShareSampleService - Interface in net.sourceforge.seqware.common.business
-
ShareSampleService interface.
- ShareSampleServiceImpl - Class in net.sourceforge.seqware.common.business.impl
-
ShareSampleServiceImpl class.
- ShareSampleServiceImpl() - Constructor for class net.sourceforge.seqware.common.business.impl.ShareSampleServiceImpl
-
- ShareStudy - Class in io.seqware.webservice.generated.model
-
- ShareStudy() - Constructor for class io.seqware.webservice.generated.model.ShareStudy
-
- ShareStudy(Integer) - Constructor for class io.seqware.webservice.generated.model.ShareStudy
-
- ShareStudy(Integer, Date) - Constructor for class io.seqware.webservice.generated.model.ShareStudy
-
- ShareStudy - Class in net.sourceforge.seqware.common.model
-
ShareStudy class.
- ShareStudy() - Constructor for class net.sourceforge.seqware.common.model.ShareStudy
-
Constructor for ShareStudy.
- ShareStudyDAO - Interface in net.sourceforge.seqware.common.dao
-
ShareStudyDAO interface.
- ShareStudyDAOHibernate - Class in net.sourceforge.seqware.common.dao.hibernate
-
ShareStudyDAOHibernate class.
- ShareStudyDAOHibernate() - Constructor for class net.sourceforge.seqware.common.dao.hibernate.ShareStudyDAOHibernate
-
Constructor for ShareStudyDAOHibernate.
- ShareStudyFacadeREST - Class in io.seqware.webservice.generated.controller
-
- ShareStudyFacadeREST() - Constructor for class io.seqware.webservice.generated.controller.ShareStudyFacadeREST
-
- ShareStudyService - Interface in net.sourceforge.seqware.common.business
-
ShareStudyService interface.
- ShareStudyServiceImpl - Class in net.sourceforge.seqware.common.business.impl
-
ShareStudyServiceImpl class.
- ShareStudyServiceImpl() - Constructor for class net.sourceforge.seqware.common.business.impl.ShareStudyServiceImpl
-
Constructor for ShareStudyServiceImpl.
- ShareValidatorController - Class in net.sourceforge.solexatools.webapp.controller
-
ShareValidatorController class.
- ShareValidatorController() - Constructor for class net.sourceforge.solexatools.webapp.controller.ShareValidatorController
-
Constructor for ShareValidatorController.
- ShareWorkflowRun - Class in io.seqware.webservice.generated.model
-
- ShareWorkflowRun() - Constructor for class io.seqware.webservice.generated.model.ShareWorkflowRun
-
- ShareWorkflowRun(Integer) - Constructor for class io.seqware.webservice.generated.model.ShareWorkflowRun
-
- ShareWorkflowRun(Integer, Date) - Constructor for class io.seqware.webservice.generated.model.ShareWorkflowRun
-
- ShareWorkflowRun - Class in net.sourceforge.seqware.common.model
-
ShareWorkflowRun class.
- ShareWorkflowRun() - Constructor for class net.sourceforge.seqware.common.model.ShareWorkflowRun
-
Constructor for ShareWorkflowRun.
- ShareWorkflowRunDAO - Interface in net.sourceforge.seqware.common.dao
-
ShareWorkflowRunDAO interface.
- ShareWorkflowRunDAOHibernate - Class in net.sourceforge.seqware.common.dao.hibernate
-
ShareWorkflowRunDAOHibernate class.
- ShareWorkflowRunDAOHibernate() - Constructor for class net.sourceforge.seqware.common.dao.hibernate.ShareWorkflowRunDAOHibernate
-
Constructor for ShareWorkflowRunDAOHibernate.
- ShareWorkflowRunFacadeREST - Class in io.seqware.webservice.generated.controller
-
- ShareWorkflowRunFacadeREST() - Constructor for class io.seqware.webservice.generated.controller.ShareWorkflowRunFacadeREST
-
- ShareWorkflowRunService - Interface in net.sourceforge.seqware.common.business
-
ShareWorkflowRunService interface.
- ShareWorkflowRunServiceImpl - Class in net.sourceforge.seqware.common.business.impl
-
ShareWorkflowRunServiceImpl class.
- ShareWorkflowRunServiceImpl() - Constructor for class net.sourceforge.seqware.common.business.impl.ShareWorkflowRunServiceImpl
-
Constructor for ShareWorkflowRunServiceImpl.
- SHOW_STATUS - Static variable in class net.sourceforge.seqware.pipeline.plugins.SymLinkFileReporter
-
- SignUpController - Class in net.sourceforge.solexatools.webapp.controller
-
RegistrationSetupController
This is invoked upon entry to Registration.jsp or RegistrationUpdate.jsp
- SignUpController() - Constructor for class net.sourceforge.solexatools.webapp.controller.SignUpController
-
Constructor for SignUpController.
- SimpleFileLock - Class in net.sourceforge.seqware.common.util.filetools.lock
-
Deprecated.
- SimpleFileLock(String) - Constructor for class net.sourceforge.seqware.common.util.filetools.lock.SimpleFileLock
-
Deprecated.
Constructor for SimpleFileLock.
- SimpleFileLock(File) - Constructor for class net.sourceforge.seqware.common.util.filetools.lock.SimpleFileLock
-
Deprecated.
Constructor for SimpleFileLock.
- size - Variable in class net.sourceforge.seqware.pipeline.modules.utilities.ProvisionFiles
-
- size - Variable in class net.sourceforge.seqware.pipeline.modules.utilities.S3CreateFileURLs
-
- size - Variable in class net.sourceforge.seqware.pipeline.modules.utilities.S3DeleteFiles
-
- size - Variable in class net.sourceforge.seqware.pipeline.modules.utilities.S3ListFiles
-
- SIZE_COUNT_FILE - Static variable in class net.sourceforge.solexatools.util.PaginationUtil
-
Constant SIZE_COUNT_FILE=5
- SIZE_COUNT_TREE - Static variable in class net.sourceforge.solexatools.util.PaginationUtil
-
Constant SIZE_COUNT_TREE=20
- sleep(int) - Static method in class net.sourceforge.seqware.common.util.processtools.ProcessTools
-
sleep.
- someString() - Method in class net.sourceforge.seqware.webservice.resources.tables.LibraryResource
-
someString.
- SORT_NAME - Static variable in class net.sourceforge.solexatools.webapp.controller.SequencerRunReportTableController
-
Constant SORT_NAME="sortname"
- SORT_NAME - Static variable in class net.sourceforge.solexatools.webapp.controller.StudyReportBoxController
-
Constant SORT_NAME="sortname"
- SORT_NAME - Static variable in class net.sourceforge.solexatools.webapp.controller.StudyReportTableController
-
Constant SORT_NAME="sortname"
- SORT_ORDER - Static variable in class net.sourceforge.solexatools.webapp.controller.SequencerRunReportTableController
-
Constant SORT_ORDER="sortorder"
- SORT_ORDER - Static variable in class net.sourceforge.solexatools.webapp.controller.StudyReportBoxController
-
Constant SORT_ORDER="sortorder"
- SORT_ORDER - Static variable in class net.sourceforge.solexatools.webapp.controller.StudyReportTableController
-
Constant SORT_ORDER="sortorder"
- SORT_ORDER_ASC - Static variable in class net.sourceforge.solexatools.webapp.controller.SequencerRunReportTableController
-
Constant SORT_ORDER_ASC="asc"
- SORT_ORDER_ASC - Static variable in class net.sourceforge.solexatools.webapp.controller.StudyReportTableController
-
Constant SORT_ORDER_ASC="asc"
- SORT_ORDER_DESC - Static variable in class net.sourceforge.solexatools.webapp.controller.SequencerRunReportTableController
-
Constant SORT_ORDER_DESC="desc"
- SORT_ORDER_DESC - Static variable in class net.sourceforge.solexatools.webapp.controller.StudyReportTableController
-
Constant SORT_ORDER_DESC="desc"
- spaceSeparateMy(Collection<String>) - Method in class net.sourceforge.seqware.pipeline.deciders.BasicDecider
-
- splitFile(File, ArrayList<File>, int) - Static method in class net.sourceforge.seqware.common.util.filetools.FileTools
-
splitFile.
- SQLQUERYFAILED - Static variable in class net.sourceforge.seqware.common.module.ReturnValue
-
Constant SQLQUERYFAILED=82
- SqwFile - Class in net.sourceforge.seqware.pipeline.workflowV2.model
-
a file object which has all information for provision
- SqwFile() - Constructor for class net.sourceforge.seqware.pipeline.workflowV2.model.SqwFile
-
- stackTraceToString(Throwable) - Static method in class net.sourceforge.seqware.common.util.exceptiontools.ExceptionTools
-
stackTraceToString.
- standard - Variable in enum net.sourceforge.seqware.pipeline.plugins.fileprovenance.ProvenanceUtility.HumanProvenanceFilters
-
- startCommand(Map<String, String>, String) - Static method in class net.sourceforge.seqware.common.util.runtools.RunTools
-
startCommand.
- startCommand(String) - Static method in class net.sourceforge.seqware.common.util.runtools.RunTools
-
startCommand.
- startCommand(String[]) - Static method in class net.sourceforge.seqware.common.util.runtools.RunTools
-
startCommand.
- startCommand(Map<String, String>, String[]) - Static method in class net.sourceforge.seqware.common.util.runtools.RunTools
-
An alternate runner that launches a process and returns it so that the
caller can process it's output directly.
- status - Variable in exception net.sourceforge.seqware.common.util.ExitException
-
- statusCounts - Variable in class net.sourceforge.seqware.common.util.workflowtools.WorkflowTools
-
- stderr - Variable in class net.sourceforge.seqware.common.module.ReturnValue
-
- stderr(String) - Static method in class net.sourceforge.seqware.common.util.Log
-
stderr.
- StdErr - Class in net.sourceforge.seqware.common.util.processtools.stderr
-
StdErr class.
- StdErr() - Constructor for class net.sourceforge.seqware.common.util.processtools.stderr.StdErr
-
- stderr2string(Process) - Static method in class net.sourceforge.seqware.common.util.processtools.stderr.StdErr
-
stderr2string.
- StderrRedirect - Annotation Type in net.sourceforge.seqware.pipeline.module
-
Annotation type to tag where to start Stderr redirect
Created by IntelliJ IDEA.
- stdout - Variable in class net.sourceforge.seqware.common.module.ReturnValue
-
- stdout(String) - Static method in class net.sourceforge.seqware.common.util.Log
-
stdout.
- StdOut - Class in net.sourceforge.seqware.common.util.processtools.stdout
-
StdOut class.
- StdOut() - Constructor for class net.sourceforge.seqware.common.util.processtools.stdout.StdOut
-
- stdout2file(Process, File, boolean) - Static method in class net.sourceforge.seqware.common.util.processtools.stdout.StdOut
-
stdout2file.
- stdout2file(Process, ArrayList<File>, boolean, int) - Static method in class net.sourceforge.seqware.common.util.processtools.stdout.StdOut
-
stdout2file.
- stdout2fileBinary(Process, File) - Static method in class net.sourceforge.seqware.common.util.processtools.stdout.StdOut
-
stdout2fileBinary.
- stdout2fileBinary(Process, ArrayList<File>, int) - Static method in class net.sourceforge.seqware.common.util.processtools.stdout.StdOut
-
stdout2fileBinary.
- stdout2fileEncoded(Process, File) - Static method in class net.sourceforge.seqware.common.util.processtools.stdout.StdOut
-
stdout2fileEncoded.
- stdout2fileEncoded(Process, ArrayList<File>, int) - Static method in class net.sourceforge.seqware.common.util.processtools.stdout.StdOut
-
stdout2fileEncoded.
- stdout2fileEncodedStripQualPrimer(Process, ArrayList<File>, int) - Static method in class net.sourceforge.seqware.common.util.processtools.stdout.StdOut
-
stdout2fileEncodedStripQualPrimer.
- STDOUTERR - Static variable in class net.sourceforge.seqware.common.module.ReturnValue
-
Constant STDOUTERR=90
- StdoutRedirect - Annotation Type in net.sourceforge.seqware.pipeline.module
-
Interface for declaring when to do the
Created by IntelliJ IDEA.
- stdoutWithTime(String) - Static method in class net.sourceforge.seqware.common.util.Log
-
Output to stdout with the time pre-pended
- stop() - Static method in class net.sourceforge.seqware.queryengine.webservice.controller.SeqWareWebServiceMain
-
stop.
- Str - Class in net.sourceforge.seqware.common.util
-
- Str() - Constructor for class net.sourceforge.seqware.common.util.Str
-
- Str.UnsafeName - Exception in net.sourceforge.seqware.common.util
-
- Str.UnsafeName(String) - Constructor for exception net.sourceforge.seqware.common.util.Str.UnsafeName
-
- StringUtils - Class in net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus
-
StringUtils class.
- StringUtils() - Constructor for class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.StringUtils
-
- stripInvalidXmlCharacters(String) - Static method in class net.sourceforge.seqware.pipeline.plugins.WorkflowStatusChecker
-
Stolen from
https://stackoverflow.com/questions/93655/stripping-invalid-xml-characters-in-java/9635310#9635310
- Studies - Class in io.seqware
-
- Studies() - Constructor for class io.seqware.Studies
-
- studiesTsv() - Static method in class io.seqware.Studies
-
- Study - Class in io.seqware.webservice.generated.model
-
- Study() - Constructor for class io.seqware.webservice.generated.model.Study
-
- Study(Integer) - Constructor for class io.seqware.webservice.generated.model.Study
-
- Study(Integer, String, String, String, int, Date) - Constructor for class io.seqware.webservice.generated.model.Study
-
- Study - Class in net.sourceforge.seqware.common.model
-
- Study() - Constructor for class net.sourceforge.seqware.common.model.Study
-
Constructor for Study.
- STUDY_ATTRIBUTES - Static variable in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles
-
Constant STUDY_ATTRIBUTES="Header.STUDY_ATTRIBUTES.getTitle()"
- STUDY_ID - Static variable in class net.sourceforge.solexatools.webapp.controller.StudyReportBoxController
-
Constant STUDY_ID="study_id"
- STUDY_ID - Static variable in class net.sourceforge.solexatools.webapp.controller.StudyReportTableController
-
Constant STUDY_ID="study_id"
- STUDY_PREFIX - Static variable in class net.sourceforge.solexatools.util.Constant
-
Constant STUDY_PREFIX="study_"
- STUDY_SWA - Static variable in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles
-
Constant STUDY_SWA="Header.STUDY_SWA.getTitle()"
- STUDY_TAG_PREFIX - Static variable in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles
-
Constant STUDY_TAG_PREFIX="Header.STUDY_TAG_PREFIX.getTitle()"
- STUDY_TITLE - Static variable in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles
-
Constant STUDY_TITLE="Header.STUDY_TITLE.getTitle()"
- STUDY_VIEW - Static variable in class net.sourceforge.solexatools.util.Constant
-
Constant STUDY_VIEW="redirect:/myStudyList.htm"
- StudyAttribute - Class in io.seqware.webservice.generated.model
-
- StudyAttribute() - Constructor for class io.seqware.webservice.generated.model.StudyAttribute
-
- StudyAttribute(Integer) - Constructor for class io.seqware.webservice.generated.model.StudyAttribute
-
- StudyAttribute(Integer, String, String) - Constructor for class io.seqware.webservice.generated.model.StudyAttribute
-
- StudyAttribute - Class in net.sourceforge.seqware.common.model
-
StudyAttribute generated by hbm2java
- StudyAttribute() - Constructor for class net.sourceforge.seqware.common.model.StudyAttribute
-
Constructor for StudyAttribute.
- StudyAttribute(int, Study, String, String) - Constructor for class net.sourceforge.seqware.common.model.StudyAttribute
-
Constructor for StudyAttribute.
- StudyAttribute(int, Study, String, String, String) - Constructor for class net.sourceforge.seqware.common.model.StudyAttribute
-
Constructor for StudyAttribute.
- StudyAttributeDAO - Interface in net.sourceforge.seqware.common.dao
-
StudyAttributeDAO interface.
- StudyAttributeDAOHibernate - Class in net.sourceforge.seqware.common.dao.hibernate
-
StudyAttributeDAOHibernate class.
- StudyAttributeDAOHibernate() - Constructor for class net.sourceforge.seqware.common.dao.hibernate.StudyAttributeDAOHibernate
-
- StudyAttributeFacadeREST - Class in io.seqware.webservice.generated.controller
-
- StudyAttributeFacadeREST() - Constructor for class io.seqware.webservice.generated.controller.StudyAttributeFacadeREST
-
- StudyBuildTree - Class in net.sourceforge.solexatools.util
-
StudyBuildTree class.
- StudyBuildTree() - Constructor for class net.sourceforge.solexatools.util.StudyBuildTree
-
- StudyController - Class in net.sourceforge.solexatools.webapp.controller
-
StudyController
- StudyController() - Constructor for class net.sourceforge.solexatools.webapp.controller.StudyController
-
Constructor for StudyController.
- StudyController(Object) - Constructor for class net.sourceforge.solexatools.webapp.controller.StudyController
-
Constructor for StudyController.
- StudyDAO - Interface in net.sourceforge.seqware.common.dao
-
StudyDAO interface.
- StudyDAOHibernate - Class in net.sourceforge.seqware.common.dao.hibernate
-
StudyDAOHibernate class.
- StudyDAOHibernate() - Constructor for class net.sourceforge.seqware.common.dao.hibernate.StudyDAOHibernate
-
Constructor for StudyDAOHibernate.
- StudyFacadeREST - Class in io.seqware.webservice.generated.controller
-
- StudyFacadeREST() - Constructor for class io.seqware.webservice.generated.controller.StudyFacadeREST
-
- StudyHtmlUtil - Class in net.sourceforge.solexatools.util
-
StudyHtmlUtil class.
- StudyHtmlUtil() - Constructor for class net.sourceforge.solexatools.util.StudyHtmlUtil
-
- StudyIdFilesResource - Class in net.sourceforge.seqware.webservice.resources.queries
-
StudyIdFilesResource class.
- StudyIdFilesResource(Context) - Constructor for class net.sourceforge.seqware.webservice.resources.queries.StudyIdFilesResource
-
Constructor for StudyIdFilesResource.
- StudyIdFilesTSVResource - Class in net.sourceforge.seqware.webservice.resources.queries
-
StudyIdFilesTSVResource class.
- StudyIdFilesTSVResource(Context) - Constructor for class net.sourceforge.seqware.webservice.resources.queries.StudyIdFilesTSVResource
-
Constructor for StudyIdFilesTSVResource.
- StudyIDResource - Class in net.sourceforge.seqware.webservice.resources.tables
-
StudyIDResource class.
- StudyIDResource() - Constructor for class net.sourceforge.seqware.webservice.resources.tables.StudyIDResource
-
Constructor for StudyIDResource.
- StudyLink - Class in io.seqware.webservice.generated.model
-
- StudyLink() - Constructor for class io.seqware.webservice.generated.model.StudyLink
-
- StudyLink(Integer) - Constructor for class io.seqware.webservice.generated.model.StudyLink
-
- StudyLink(Integer, String, String) - Constructor for class io.seqware.webservice.generated.model.StudyLink
-
- StudyLink - Class in net.sourceforge.seqware.common.model
-
StudyLink generated by hbm2java
- StudyLink() - Constructor for class net.sourceforge.seqware.common.model.StudyLink
-
Constructor for StudyLink.
- StudyLink(int, Study, String, String) - Constructor for class net.sourceforge.seqware.common.model.StudyLink
-
Constructor for StudyLink.
- StudyLink(int, Study, String, String, String, String) - Constructor for class net.sourceforge.seqware.common.model.StudyLink
-
Constructor for StudyLink.
- StudyLinkDAO - Interface in net.sourceforge.seqware.common.dao
-
StudyLinkDAO interface.
- StudyLinkDAOHibernate - Class in net.sourceforge.seqware.common.dao.hibernate
-
StudyLinkDAOHibernate class.
- StudyLinkDAOHibernate() - Constructor for class net.sourceforge.seqware.common.dao.hibernate.StudyLinkDAOHibernate
-
- StudyLinkFacadeREST - Class in io.seqware.webservice.generated.controller
-
- StudyLinkFacadeREST() - Constructor for class io.seqware.webservice.generated.controller.StudyLinkFacadeREST
-
- StudyList - Class in net.sourceforge.seqware.common.model.lists
-
StudyList class.
- StudyList() - Constructor for class net.sourceforge.seqware.common.model.lists.StudyList
-
Constructor for StudyList.
- StudyListController - Class in net.sourceforge.solexatools.webapp.controller
-
RegistrationSetupController
- StudyListController() - Constructor for class net.sourceforge.solexatools.webapp.controller.StudyListController
-
Constructor for StudyListController.
- StudyListDetailsController - Class in net.sourceforge.solexatools.webapp.controller
-
StudyListDetailsController class.
- StudyListDetailsController() - Constructor for class net.sourceforge.solexatools.webapp.controller.StudyListDetailsController
-
Constructor for StudyListDetailsController.
- StudyListDetailsFlatController - Class in net.sourceforge.solexatools.webapp.controller
-
- StudyListDetailsFlatController() - Constructor for class net.sourceforge.solexatools.webapp.controller.StudyListDetailsFlatController
-
- StudyReportBoxController - Class in net.sourceforge.solexatools.webapp.controller
-
StudyReportBoxController class.
- StudyReportBoxController() - Constructor for class net.sourceforge.solexatools.webapp.controller.StudyReportBoxController
-
- StudyReportController - Class in net.sourceforge.solexatools.webapp.controller
-
RegistrationSetupController
- StudyReportController() - Constructor for class net.sourceforge.solexatools.webapp.controller.StudyReportController
-
Constructor for StudyReportController.
- StudyReportSetupController - Class in net.sourceforge.solexatools.webapp.controller
-
StudyReportSetupController class.
- StudyReportSetupController() - Constructor for class net.sourceforge.solexatools.webapp.controller.StudyReportSetupController
-
- StudyReportTableController - Class in net.sourceforge.solexatools.webapp.controller
-
StudyReportTableController class.
- StudyReportTableController() - Constructor for class net.sourceforge.solexatools.webapp.controller.StudyReportTableController
-
Constructor for StudyReportTableController.
- StudyResource - Class in net.sourceforge.seqware.webservice.resources.tables
-
StudyResource class.
- StudyResource() - Constructor for class net.sourceforge.seqware.webservice.resources.tables.StudyResource
-
Constructor for StudyResource.
- StudySampleReportFileLineItem - Class in net.sourceforge.solexatools.webapp.metamodel
-
StudySampleReportFileLineItem class.
- StudySampleReportFileLineItem(Sample, Sample, IUS, File) - Constructor for class net.sourceforge.solexatools.webapp.metamodel.StudySampleReportFileLineItem
-
Constructor for StudySampleReportFileLineItem.
- StudySampleReportLineItem - Class in net.sourceforge.solexatools.webapp.metamodel
-
StudySampleReportLineItem class.
- StudySampleReportLineItem(Sample, Sample, String[]) - Constructor for class net.sourceforge.solexatools.webapp.metamodel.StudySampleReportLineItem
-
Constructor for StudySampleReportLineItem.
- StudyService - Interface in net.sourceforge.seqware.common.business
-
StudyService interface.
- StudyServiceImpl - Class in net.sourceforge.seqware.common.business.impl
-
StudyServiceImpl class.
- StudyServiceImpl() - Constructor for class net.sourceforge.seqware.common.business.impl.StudyServiceImpl
-
Constructor for StudyServiceImpl.
- StudySetupController - Class in net.sourceforge.solexatools.webapp.controller
-
RegistrationSetupController
- StudySetupController() - Constructor for class net.sourceforge.solexatools.webapp.controller.StudySetupController
-
Constructor for StudySetupController.
- StudyTableController - Class in net.sourceforge.solexatools.webapp.controller
-
RegistrationSetupController
- StudyTableController() - Constructor for class net.sourceforge.solexatools.webapp.controller.StudyTableController
-
Constructor for AnalisysListController.
- StudyTableControllerDetails - Class in net.sourceforge.solexatools.webapp.controller
-
TODO:
* it would be best if this controller would actually render the workflow_runs
too.
- StudyTableControllerDetails() - Constructor for class net.sourceforge.solexatools.webapp.controller.StudyTableControllerDetails
-
Constructor for AnalisysListController.
- StudyType - Class in io.seqware.webservice.generated.model
-
- StudyType() - Constructor for class io.seqware.webservice.generated.model.StudyType
-
- StudyType(Integer) - Constructor for class io.seqware.webservice.generated.model.StudyType
-
- StudyType(Integer, String) - Constructor for class io.seqware.webservice.generated.model.StudyType
-
- StudyType - Class in net.sourceforge.seqware.common.model
-
StudyType class.
- StudyType() - Constructor for class net.sourceforge.seqware.common.model.StudyType
-
- StudyTypeDAO - Interface in net.sourceforge.seqware.common.dao
-
StudyTypeDAO interface.
- StudyTypeDAOHibernate - Class in net.sourceforge.seqware.common.dao.hibernate
-
StudyTypeDAOHibernate class.
- StudyTypeDAOHibernate() - Constructor for class net.sourceforge.seqware.common.dao.hibernate.StudyTypeDAOHibernate
-
Constructor for StudyTypeDAOHibernate.
- StudyTypeFacadeREST - Class in io.seqware.webservice.generated.controller
-
- StudyTypeFacadeREST() - Constructor for class io.seqware.webservice.generated.controller.StudyTypeFacadeREST
-
- StudyTypeList - Class in net.sourceforge.seqware.common.model.lists
-
StudyTypeList class.
- StudyTypeList() - Constructor for class net.sourceforge.seqware.common.model.lists.StudyTypeList
-
Constructor for StudyTypeList.
- StudyTypeResource - Class in net.sourceforge.seqware.webservice.resources.tables
-
ExperimentResource class.
- StudyTypeResource() - Constructor for class net.sourceforge.seqware.webservice.resources.tables.StudyTypeResource
-
Constructor for ExperimentResource.
- StudyTypeService - Interface in net.sourceforge.seqware.common.business
-
StudyTypeService interface.
- StudyTypeServiceImpl - Class in net.sourceforge.seqware.common.business.impl
-
StudyTypeServiceImpl class.
- StudyTypeServiceImpl() - Constructor for class net.sourceforge.seqware.common.business.impl.StudyTypeServiceImpl
-
Constructor for StudyTypeServiceImpl.
- StudyUpdateValidator - Class in net.sourceforge.solexatools.validation
-
- StudyUpdateValidator() - Constructor for class net.sourceforge.solexatools.validation.StudyUpdateValidator
-
- StudyValidator - Class in net.sourceforge.solexatools.validation
-
StudyValidator class.
- StudyValidator() - Constructor for class net.sourceforge.solexatools.validation.StudyValidator
-
Constructor for StudyValidator.
- subList(int, int, List) - Static method in class net.sourceforge.solexatools.util.PaginationUtil
-
subList.
- subList(HttpServletRequest, String, List<T>) - Static method in class net.sourceforge.solexatools.util.PaginationUtil
-
subList.
- subList(HttpServletRequest, String, int, List<T>) - Static method in class net.sourceforge.solexatools.util.PaginationUtil
-
subList.
- subListSD(HttpServletRequest, String, List) - Static method in class net.sourceforge.solexatools.util.PaginationUtil
-
subListSD.
- submitCancel(int) - Static method in class io.seqware.WorkflowRuns
-
- submitRetry(int) - Static method in class io.seqware.WorkflowRuns
-
- SUCCESS - Static variable in class net.sourceforge.seqware.common.module.ReturnValue
-
Constant SUCCESS=0
- SummaryData - Class in net.sourceforge.solexatools.util
-
SummaryData class.
- SummaryData() - Constructor for class net.sourceforge.solexatools.util.SummaryData
-
Constructor for SummaryData.
- SummaryLaunchWorkflowController - Class in net.sourceforge.solexatools.webapp.controller
-
SummaryLaunchWorkflowController class.
- SummaryLaunchWorkflowController() - Constructor for class net.sourceforge.solexatools.webapp.controller.SummaryLaunchWorkflowController
-
Constructor for SummaryLaunchWorkflowController.
- SummaryLaunchWorkflowController(Object) - Constructor for class net.sourceforge.solexatools.webapp.controller.SummaryLaunchWorkflowController
-
Constructor for SummaryLaunchWorkflowController.
- SummaryLine - Class in net.sourceforge.solexatools.util
-
SummaryLine class.
- SummaryLine() - Constructor for class net.sourceforge.solexatools.util.SummaryLine
-
Constructor for SummaryLine.
- supports(Class) - Method in class net.sourceforge.solexatools.validation.ExperimentValidator
- supports(Class) - Method in class net.sourceforge.solexatools.validation.LaneValidator
- supports(Class) - Method in class net.sourceforge.solexatools.validation.LoginValidator
-
Returns true if this Validator supports the
specified Class, and false otherwise.
- supports(Class) - Method in class net.sourceforge.solexatools.validation.SampleValidator
- supports(Class) - Method in class net.sourceforge.solexatools.validation.SequencerRunValidator
- supports(Class) - Method in class net.sourceforge.solexatools.validation.SequencerRunWizardValidator
- supports(Class) - Method in class net.sourceforge.solexatools.validation.StudyValidator
- supports(Class) - Method in class net.sourceforge.solexatools.validation.UploadFileValidator
- supports(Class) - Method in class net.sourceforge.solexatools.validation.UploadSequenceValidator
- supports(Class) - Method in class net.sourceforge.solexatools.validation.WorkflowParamValidator
- supports(Class) - Method in class net.sourceforge.solexatools.validation.WorkflowValidator
- supportsCancel(String) - Static method in class io.seqware.Engines
-
- supportsRetry(String) - Static method in class io.seqware.Engines
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- SwBadFileException - Exception in net.sourceforge.seqware.common.err
-
Created by IntelliJ IDEA.
- SwBadFileException() - Constructor for exception net.sourceforge.seqware.common.err.SwBadFileException
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Constructor for SwBadFileException.
- SwBadFileException(String) - Constructor for exception net.sourceforge.seqware.common.err.SwBadFileException
-
Constructor for SwBadFileException.
- SwBadFileException(String, Throwable) - Constructor for exception net.sourceforge.seqware.common.err.SwBadFileException
-
Constructor for SwBadFileException.
- SwBadFileException(Throwable) - Constructor for exception net.sourceforge.seqware.common.err.SwBadFileException
-
Constructor for SwBadFileException.
- SwBadModuleException - Exception in net.sourceforge.seqware.common.err
-
User: Xiaoshu Wang (xiao@renci.org)
Date: 9/1/11
Time: 2:56 PM
- SwBadModuleException() - Constructor for exception net.sourceforge.seqware.common.err.SwBadModuleException
-
Constructor for SwBadModuleException.
- SwBadModuleException(String) - Constructor for exception net.sourceforge.seqware.common.err.SwBadModuleException
-
Constructor for SwBadModuleException.
- SwBadModuleException(String, Throwable) - Constructor for exception net.sourceforge.seqware.common.err.SwBadModuleException
-
Constructor for SwBadModuleException.
- SwBadModuleException(Throwable) - Constructor for exception net.sourceforge.seqware.common.err.SwBadModuleException
-
Constructor for SwBadModuleException.
- SwParameterException - Exception in net.sourceforge.seqware.common.err
-
Created by IntelliJ IDEA.
- SwParameterException() - Constructor for exception net.sourceforge.seqware.common.err.SwParameterException
-
Constructor for SwParameterException.
- SwParameterException(String) - Constructor for exception net.sourceforge.seqware.common.err.SwParameterException
-
Constructor for SwParameterException.
- SwParameterException(String, Throwable) - Constructor for exception net.sourceforge.seqware.common.err.SwParameterException
-
Constructor for SwParameterException.
- SwParameterException(Throwable) - Constructor for exception net.sourceforge.seqware.common.err.SwParameterException
-
Constructor for SwParameterException.
- SwRunnerParameterException - Exception in net.sourceforge.seqware.common.err
-
User: Xiaoshu Wang (xiao@renci.org)
Date: 9/6/11
Time: 3:20 PM
- SwRunnerParameterException() - Constructor for exception net.sourceforge.seqware.common.err.SwRunnerParameterException
-
Constructor for SwRunnerParameterException.
- SwRunnerParameterException(String) - Constructor for exception net.sourceforge.seqware.common.err.SwRunnerParameterException
-
Constructor for SwRunnerParameterException.
- SwRunnerParameterException(String, Throwable) - Constructor for exception net.sourceforge.seqware.common.err.SwRunnerParameterException
-
Constructor for SwRunnerParameterException.
- SwRunnerParameterException(Throwable) - Constructor for exception net.sourceforge.seqware.common.err.SwRunnerParameterException
-
Constructor for SwRunnerParameterException.
- symDifference(Set<T>, Set<T>) - Static method in class net.sourceforge.seqware.pipeline.tools.SetOperations
-
- SymLinkFileReporter - Class in net.sourceforge.seqware.pipeline.plugins
-
SymLinkFileReporter class.
- SymLinkFileReporter() - Constructor for class net.sourceforge.seqware.pipeline.plugins.SymLinkFileReporter
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Constructor for SymLinkFileReporter.